Hey to a fellow Gen-2 oddball. It may be best practice on this site to ALWAYS identify that you're not tuning an LS engine. Alvin is one of the few that knows us.
Something like this:
Warning: Frankenstein!!!! A GM Gen III PCM talking to a GM Gen-2 engine, Oh My!
Few things I see in the last tune:
Injector data don't look right for a stock LT1; IFR should be 24.9 and Voltage offsets are wrong.
Cylinder volume is smaller than a stock LT1; should be 717.25 ml/Cyl
Airflow: It looks like both the MAF and VE are too high, esp. at idle and cruise.
OL EQ ratio is all over the place, like stock. You're aiming at a moving target.
Also, you can tune VE and MAF at the same time using Dynamic Air and use STFT. The reason people like using the NBO2's is because they're accurate at Stoich, and your goal should be Stoich until you get to WOT.
Don't worry about transients until after the VE and MAF are calibrated. That's in one table under fuel transients. You'll likely never get rid of the momentary lean spike, but you should knock it down fast.