OP, I think you already know hiking the JMT is a bad idea, and are looking for confirmation. So here it is: you may be able to grunt it out with some suffering and vitamin I, but you'll pay the price for months after. It sounds like your issues are advanced enough that you might have to bail. IMO, not worth the gamble.
It's time to write off the rest of 2013 from a hiking perspective. Even cycling is probably not a good idea for a month or so. Find a good PT who can help you track down and fix, definitively, whatever issues you have going on. Start swimming, or maybe hit the erg at the gym. Find a good yoga class. Come back strong next spring.
A decade ago I got bad IT syndrome from road running. I never let it rest enough, used vitamin I to do some trips in the face of good advice, and because of this it took the better part of 2 years for things to finally get better. It also took 2 chiros and 3 PTs before I found someone competent enough to tell me what was actually wrong (tight/weak hamstrings) and help me fix it.