John, Don't get too discouraged, but you do have to be kind of 'on your game' and know the rules to getting your permits from various agencies. You are only allowed to get your permits 24 weeks in advance from Yosemite. How flexible are you on routes and time? If there are any left for your time frame, you can get your permits from Inyo Nat'l Forest 6 months in advance and hike from Reds Meadow to Happy Isles, then take the YARTS back and hike Reds Meadows to Whitney Portal. I have found permitting much easier from Inyo. If you are not 'locked in' to the whole JMT, permits are easier to get from Tuolumne Meadows to Whitney Portal. You can also start at alternate trailheads out of Yosemite. I think the key is to research your options and be flexible with a date. Good Luck.
By the way, when were you looking at going? I am shooting for mid-August and if you are out there we may run into one another. There are also other sites that have JMT hiking groups ie; Trailjournals, YahooJMT ect.