One more update for anyone still reading:
I had reset my transmission using the hold the gas pedal to the floor for 30 seconds thing a few times and it never really made much difference. Friday I finally got my D+K CAN cable in and reset all the adaptations via INPA. First drive, it had a little trouble shifting smooth, little jerky, high RPM's once or twice before finally changing gears, etc. etc. BUT ultimately after it figured it out, basically all of my problems are gone. I've driven a few hundred miles this weekend and the 5th gear hardcore jerking is at most a small hiccup, only at a certain speed/throttle position (so seldom I haven't been able to really even repeat it, only felt it barely once by coincidence). Jerky 5 to 6 change is gone. Jerky 3 to 2 is gone. The little jerk right before you stop (2 to 1) is still present, but a software update should take care of that one. I just haven't gotten up the nerve to update the transmission computer software yet, lol.
Also, changed spark plugs today and my god the old ones looked horrible. 5 were the original bosch style (the car has 180K on it so I sure hope they aren't actually originals) and the electrodes were half gone. The other 3 (easiest ones to get to..) had been replaced at some point with NGK ones. I replaced all 8 in about an hour (not sure why everyone acts like it's a tough job? It was really relatively easy and painless).
Verdict: It's a whole different car. It used to be so jerky off idle I was almost embarassed to have people ride with me and def wouldn't let anyone else drive. I almost preferred to drive my work car (Imapala) just because this thing was such a pain to drive halfway smoothly. Between the plugs and transmission complete reset, it's completely different. So much better to drive now!
edit: added pics of sparkplugs
Last edited by schpenxel; 10-21-2012 at 02:56 PM.