I'm not super heavy on all the medical disqual stuff, so bear with me on some of the (dumb) questions.
Did they pull your NEC? I can see how a medical condition could prevent you from receiving occupational exposure (i.e. getting a TLD), but if you wish to remain a nuke, talk to your Dept Master Chief. He may know of some way to keep your NEC for a while even if you can't draw a TLD, and he may be able to use you for maintaining Dept qual folders, training records, pubs, and other stuff on the admin side of the house to at least keep you involved with nuclear stuff. And anyway, you don't really need an NEC to do nuclear admin, just a security clearance (which shouldn't get pulled for a non-psychiatric medical issue). Just a thought.
Are you currently in the no-man's-land commonly called Med Hold? If they won't let you play in the nuclear sandbox, I would recommend taking every CLEP test that you can get your hands on. Even if there ends up being not enough time to take bona-fide college courses, you can still squeeze off a ton of CLEP tests in a few months. Even if you aren't thinking of college right now, you may think of it later down the road. And anyway, CLEP tests are free while you're Active Duty, so you've got nothing to lose (and personally I'd rather be out taking CLEP tests than sitting idle in Med Hold). Do you have access to a Navy College Office where you're at? Studying for the NUF like thenukeman mentioned is another terrific idea.
And usually if you ask somebody in Medical if there is anything that you could/should be doing in regard to your waiver, 99% of the time they'll tell you "No, we're just waiting on _____". And you can usually ask "About how long does _____ usually take to turn around a waiver like mine?" without p---ing anyone off. So in two simple questions, you've determined the current status of your waiver and 'pinged' on Medical about it (squeaky wheel, and all that) - all without giving the appearance that you're pressuring a commander. Repeat every three days or so.
THIS PART I SAY VERY CAUTIOUSLY: consider talking off-line with a Navy JAG. Tell him everything about how you were brought into the Navy, and the situation you are in right now. There may not be anything that can be done, and I would NOT encourage you to jump into any kind of legal action at this point, but you should at least go and determine what your possible options are. Keep your cards very close on this issue, though; tell anybody that you are going to see Legal, and just guess what's gonna go through the back of their minds every time they see you from that point on. But at the same time, you really oughta know what your rights & options are.
Best wishes, & good luck!