Just loaded up 6.0 Touch with JB 3.6. Restoring apps now. Everything seemed to work out fine (did an entire wipe). Once I'm set up, I'll try restoring a Nandroid and see what happens.
Probably should have looked here before flashing the new CWM, but I'm usually the risk taker anyway.
Well, 3.6 didn't want to restore any apps. Going to reinstall. Restored my backup I made with 6.0 and ended up with no softkeys or notification bar.
I'll give it another shot before trying TWRP.