Jeremy,
Larry sent me his file and I believe I found the issue. He had 625 cc's in for the injector constant and is running 83# inj which should be 875cc according to Chucks handy dandy calculator. That would add about 30% more fuel and cause the problems he is having.
I also rescaled his axis tables and cleaned up the AFR and spark tables and shut the WBO2 off at idle. I have a dumb question though as I don't mess with BS3 that often. Where do you set the TPS idle and WOT values? Under hardware config it has some goofy EJET setting for TPS% 2-4 switch and 4-2, what is that for

They have a 3% TPS thershold setting that indicates idle, is that it??
Also, I thought the ignition strategy was configurable in this system but I don't see anywhere to set that stuff up
Outside of the above everything else seems pretty basic and straight forward. The software is really basic and the transient and idle tables are REALLY basic. I don't see why I can't get him idling, running and driving without much of an issue as long as the car is healthy.