"New setup, and the guy who did the setup is very fast as well"
I wonder if this is a part of your issue. Certainly something I've heard many times from racers who get the "fast guy setup". I know when Kessler sets up my car, he doesn't give me the same setup as his pro driver whose used his Miata's.
Are you now back to the set-up you were super excited about at Thompson?
Ditto on Kessler and his setup for us NA (SM) drivers - I believe he has a base set for each platform and tunes/adjusts from there based on your performance.
I'd also bet his NA ITA setup is slightly different considering the variability of shocks, spring rates, and bushings.
Sounds like you (Jeff) went to SAC and had that shop (SAC) setup your car. Perhaps the message didn't get to the guys turning the wrenches to give you "Elivan's setup"?
From what I recall seeing of his '99 and his driving style, he likes to "drive on the bumpstops", has tons of negative camber (upper eccentrics), and likes things loose so perhaps translating that over to your NA ITA car something was lost?
I hope you can get back to your regular setup shop as I know how you feel when things aren't "right" and you're fighting an ill-handling car all weekend.