Great question! I'll answer this in detail because I think others would benefit from the routine I describe below. It wouldn't allow me to edit my post above to reflect all the added info., so I just finished it and re-posted the whole thing.
What are your primary goals? Do you want to maintain a lean yet strong and muscular body, but still have sufficient muscular/cardiovascular endurance, or is your primary focus cardiovascular conditioning and muscular endurance without the addition of packing on more muscle mass?
Just from the information in your post, I have a few recommendations. You are doing things right in regards to performing your strength training 3X per week. Having 48-72 hours rest in between resistance training sessions for the same muscle groups is for proper recovery. This is MUCH more effective than training a muscle group(s) 1X per week. The way your running workouts are designed from what you told is fantastic in regards to progression and intensity changes. You want your resistance training sessions to contain the same principles. You must force the body to change instead of waiting for it to change. The longer you stay with a specified load on a given exercise for the same amount of volume the same times per week, etc. the easier it becomes for the body to build up a tolerance to the demand and stimulus being placed upon it. With that said, there are many ways to create workout routines that fit for various schedules, etc. However, it's all about we use physiological principles to create the most effective and productive strength training workouts, all while keeping the chances of falling into the ruts of exercise routines over time like plateaus, etc. A particular routine I provide for my clients, and follow myself is a resistance training routine that involves training the full body each workout 3X per week with 48 hours of rest in between training sessions. The reason to train each muscle group three times per week is to take advantage of the "window of opportunity" so-to-speak in regards to the physiological stimulus that your training session provides. Some research suggests that the stimulus from resistance training exercise may last between 48-72 hours. So, the stimulus your provided to the muscle tissue to tell it to change, specifically muscle hypertrophy (growth), but can be muscular endurance as well, and all that comes from a bout a resistance exercise such as increased mitochondria (depending upon the intensity), increased ribosome activity to synthesize protein, satellite cell activity, etc. no longer has that effect after 48-72 hours until the muscle is trained again. Many people train a single muscle group 1X per week and beat the hell out of it, but don't work it again for another 5-7 days. That's simply not ideal in regards to muscle gains if the window for the stimulus is 48-72 hours. However, the people that work it 1X per week may do so many sets that they are so unbelievably sore and weak for almost a week until they can train it again. Their muscle still need to recover from the damage that was done to it, but that stimulus to actually change and improve upon has now decreased tremendously after the 48-72 hour mark. They shouldn't see many gains after that window even though they are still beat up from their workout. Those individuals would be much more wise to lower the total volume and increase the frequency. Now, many people change their workouts much too slowly, such as the load, frequency, exercise, volume, etc. I change the routine within the same week to provide the muscle with a stimulus that is set for a particular goal.
So, the workout week will look like this (all the workouts below can be completed under an hour, and sometimes 30 minutes):
Muscular Endurance Day, Full-Body Routine: Involves performing 3-4 sets per muscle group with a load that allows at and no more than 15-20 repetitions (with perfect technique and with a tempo of say 2 seconds eccentric: aka lengthening of the muscle phase, and 1 second concentric: aka shortening of the muscle) with only 30-60 seconds max rest (unless you need more due to heart rate) between working the same muscle group for each set. So, on this day, it may be best to pick a muscle group to work, then complete ALL your sets for that muscle group one after another until you complete 3-4 sets of 15-20 reps with only 30 seconds rest in between. Now, we stay at the same exercise simply because 30 sec rest doesn't leave much time to get to another muscle group to work, and then get back to the original one all within 30 seconds, so we stick with one muscle the whole time until the sets are complete. You'll feel high levels of lactic acid and blood in the muscle tissue and you should experience some muscle discomfort, not pain, which is obviously a huge difference. Now, many people in this repetition range don't need warm-up sets since the load is so light that the chance of injury is less than lifting heavier. This rep range, volume, and rest time between sets will allow the muscle to change by responding in a manner that will allow it to perform work for an extended period of time (one of those changes is an increase in mitochondria in the muscle cells). Also, it doesn't necessarily matter what order you do the muscle groups. However, I recommend performing the larger muscle groups first, or lagging body parts at the beginning of the workout to help them achieve symmetry with the rest of the body. Also, whatever my order of muscle groups performed last week, I completely reverse and the new week I'll go from bottom of the list to the top of the list, as this allows many different muscle groups to get a more fair share of the energy allowance and strength you have during the beginning versus the end of a workout. These recommendations described in the last two sentences I also recommend for the Wednesday and Friday workouts as well.
Muscle Hypertrophy Day, Full-Body Routine: Involves performing 3 sets per muscle group with a load that allows at and no more than 8-10 repetitions (with perfect technique and with a tempo of say 2 seconds eccentric: aka lengthening of the muscle phase, and 1 second concentric: aka shortening of the muscle) with only 60-90 seconds max rest (unless you need more due to heart rate) between getting back to working the same muscle group for the next set(s). As you notice, the rest time increased just a bit due to the increase in load. However, the discomfort felt in the Monday workout should feel very similar to this one with the increased blood flow and lactic acid accumulation in the muscle due to the low rest time between sets, yet the load has been increased to provide a different stimulus to achieve our new goal of this workout more effectively. It has still not been 100% shown exactly why this repetition range and rest time stimulates hypertrophy best, but it is thought that there is a stimulation of anabolic hormones (IGF-1, and testosterone), along with the load and total volume that is sufficient enough to cause changes in cellular growth of the muscle tissue. Now, with Monday's workout, we simply stayed with the same exercise to complete all the sets before moving onto the next muscle group. On this day, we will chose two muscle groups to work between since the rest time of 60 seconds allows sufficient time to work between a pair of muscles. I recommend choosing antagonistic muscle groups, as some research suggests there may be an added effect on hypertrophy by doing so. Say we picked biceps and triceps since they are opposing, then we will now perform a set of say....standing bicep curls, and after completing the set we look and make a mental note of the clocks second hand (we'll say the we ended the set at 11:04:40PM). Immediately when we finish, we will go to a triceps exercise and perform a set of say....lying tricep barbell extensions. Check the clock and ensure you get back to your second set of bicep curls by 60 seconds, which would be 11:05:40 in our example. Complete all your sets for these pairs. Once you're done, choose the next pair of antagonistic muscle groups and complete the same process, and so on until the whole body is complete. Some antagonistic muscle groups include: pectoralis major and middle back (ex. chest press and reverse fly), latissimus dorsi and deltoids (ex. pull-ups and dumbbell lateral raise), quadriceps and hamstrings (ex. leg extension and hamstring curl), biceps and triceps (seated incline bicep curl and standing tricep press-down machine), abdominals and low back extensors (resistance band standing spinal rotations and back extension machine), and then you can do calves if needed by themselves. Now, a warm-up sets isn't necessary for Mondays workout since it's light, but this workout it's a good idea to do so. Warm-ups are always done at the beginning of a pairing and can be done within the pairs you chose. In our previous example, you'll warm up with a set of 50-60% of your 10 rep max and perform 10 of those reps, which is obviously not to fatigue for good reason since the goal is to warm up the muscle by increased blood flow, and enzyme activity. Then, warm-up with your triceps extension with 50-60% of your 10 rep max and perform 10 reps of those. Then, begin your true 8-10 rep workout as we described above
. If you need an additional warm up set, simply perform another warm up set between the pairs but use 80% of your 10 rep max and perform 6-8 reps without going to fatigue obviously.
Muscle Strength Day, Full-Body Routine: Involves performing 3 sets per muscle group with a load that allows at and no more than 5-6 repetitions (with perfect technique and with a tempo of say 2 seconds eccentric: aka lengthening of the muscle phase, and 1 second concentric: aka shortening of the muscle) with 3-4 minutes rest (unless you need more due to heart rate) between getting back to working the muscle group your began with first. You can see that the rest time is significantly more here due to the high increase in load. We want enough rest for the muscle to recoup to have strength to perform future sets in the workout, but you don't want to wait too long causing the muscle to get cold. So, we can't do the pairing we did in Wednesday's work-out. Instead, we chose four different muscle groups, and preferably not antagonistic ones, but it's okay if there are. Remember, the goal here is muscle strength, not just hypertrophy, even though hypertrophy will still be seen in this rep range. This repetition range has been shown to provide great gains in muscular strength, not only due to increases in muscular size and it's ability to withstand greater tensile forces, but also do to central nervous system adaptations that increase efficiency of contracting muscle tissue like frequency coding. So, say you chose pectoralis, quads, biceps, and abs. Before beginning your heavy sets, you'll perform warm ups sets like explained above, but you'll perform a warm-up for all 4 muscle groups you chose. After you warm-up, begin performing a set for your pects with a 5-6 rep max range, move onto your quads, then biceps, and abs all working in the 5-6 rep range until muscular fatigue. Then, start at your pecs again for set 2, then quads, biceps, and abs. Then, onto your 3rd set for the same 4 muscle groups. After that, repeat this process for another 4 muscle groups until the whole body is complete
As you can see, with this routine, we not only take advantage of physiology, we also reduce the chance of plateau considering the load progressively gets heavier throughout the week, and overload occurs over time. We never really give the muscle a chance to stagnate or allow the stimulus of a certain load to lessen because the load is changing constantly during the week. This routine also provides a well rounded physique since we train for three different muscular goals during the week, endurance, hypertrophy, and strength. In other words, we learn to perform work for longer periods of time, then we grow new muscle tissue, and then we gain even more strength with that new muscle tissue via neural pathways. As you get stronger, adjust to load so you are always working with your true, 15-20, 8-10, and 5-6 rep range. Many people just wait to see changes in strength by lifting the sameeeeee load for a long time until they can finally add a rep or so, then they add weight. We don't do that, as we tell the muscle to change via load and goal changes, and the load and rest time between sets are important for this. Think of a muscle like a callus on the hand. The callus grows because it builds a tolerance to the friction or pressure that caused it. The more you work with the hands, and the more friction and pressure it sees, it get's thicker so it doesn't get damaged as easily. So, when you lift with the same load for a muscle group over and over again, the stimulus for the muscle to change lessens. That's a primary reason why we progress in the way described above.
Also, as a side note, I keep the same exercises throughout the week for the different muscle groups because I want the chance for the muscle to feel the stress in the same exercise in each rep range throughout the week. The next week, I'll chose a completely different exercise for every muscle and do that for every rep range during that week. This doesn't have to be done, but it's something I like. You can switch it up as much as needed to keep it "fresh" so you don't find any of your workouts monotonous.
In regards to whey protein supplementation, I do prefer whey protein after workouts, as well as simple carbohydrates with it. Be sure to have carbs and protein together after your work-out. Carbohydrates are just as important immediately following a workout. Carbohydrates signal the body to shift from a catabolic mode (breaking down of molecules) to an anabolic mode (building of molecules) with a sharp shift in insulin, which means it's in "recovery" mode now. After a workout, your natural hormone levels go a bit haywire (testosterone will decrease as the workout goes on and cortisol increases). Cortisol is a stress hormone that will eventually use protein (amino acids) for energy when it sees stored carbs (aka glycogen) in the muscle and liver get lower during the workout. Therefore, you are degrading more muscle tissue than needed during the workout, and producing more waste products, and reducing recovery rate, and potential for new growth of lean tissue. A great way to lessen this effect DURING your workout is to drink a sports drink with simple sugars, electrolytes, and vitamins and minerals. It may be beneficial to have a drink that contains somewhere around 25-30 grams of carbs and 3-5 grams of whey protein (this small amount of protein also helps to lessen muscle degradation during workouts, but as you can see it doesn't take much), which I believe is information provided by several great sports dieticians that wrote a book on the timing of nutrients before, during, and exercise (if you need the name of the book let me know and I'll get the title and authors names for you). There are many different brands out there, and non I am particularly partial too, but it's a little more difficult finding a carb sports drink that also has a small of protein in it, but Accelerade does and some others. Other wise, find a sports drink like Gatorade that's widely available and put your own whey protein in it in the small amount listed. Simple carbs are very easy to digest, allows very quick energy to be had for the muscles to use, and keep insulin levels higher during the workout to lessen muscle degradation, keep cortisol at bay, among many other things, and fuel your work-out. Now for after your work-out, a ratio of 3-1 or 4-1 of carbs to protein after a work out is the recommended amount by many professionals, as this causes a great shift in insulin and sparks recovery on a large level. The carbs should also be simple sugars and as close to glucose as possible, and make sure your post work-out drink or food doesn't contain fiber, and contains minimal if any fat. A sports drink in this scenario works well again because it contains simple sugars, micronutrients, and electrolytes. Except now, we want roughly 60-80 grams of high Glycemic index (GI) carbs and 20 grams of Whey protein (because it's bio-availability is great, it digest very quickly, and has essential amino acids considering it's from dairy) after a workout, but the amount needed may also change if a long endurance event has been performed. The numbers above are assuming your worked out for about an hour or so.
I hope all this helps. I know it's a lot to digest, but it all becomes very simple to do and understand with very little time and practice.