1. The Navy/USMC/USCG are very rigid about color vision. The USAF is probably not much better. But they have used different tests than the FAA in the past, so you might have a chance. I believe they will let you try more than one type of test. But if you fail the military test(s) you are done...there are no waivers that I have ever heard of, and your FAA medical is meaningless to the military. About all you can do is take the test and see what happens.
2. I suspect there are probably no military aviators who have a "history of allergies since age 12". The trick is to not have a history...hint, hint.