Military flight physicals are significantly more thorough and stringent than class 2 or class 3 FAA physicals. Can't speak to a 1st class, as I haven't had one yet, but I'd venture a guess that the mil physical is at least as stringent, if not more. For the USN side, you do vision screening (20/40 correctable to 20/20 with no color blindness or significant astigmatism or glaucoma), blood work, EKG, hearing test, anthro measurements (body size stuff), X-rays (especially if you have a history of allergies or sinus issues), as well as a few other odds and ends. If the FAA isn't letting you fly, suffice to say that the military won't be either, though there are waiver processes available in each realm, and I don't know specifically what is holding you up, so I guess that would depend.