Well I switched back to an auto tune and it seems much happier. It's using all of the In Gear tables now rather than just some of them. I am using f-body manual throttle cracker and follower settings, they need some slight tweaking but overall they work great.
2001 Silverado 5.3L ECSB 2WD T56:
T76 turbo, Meth injection, 72# injectors, 799 heads, 212/212 114LSA cam, Built 4L80E, 3.42's
EFILive V1 Commercial, COS5 2-bar SOLSD, AEM wideband
I can confirm that my factory manual 99 ls1 using os5 also uses the throttle follower P/N decay rate table. Everything else uses in gear tables
So your situation is not unique. FWIW Aussie ls1 cars don't use the clutch switch for the PCM either.
2001 Silverado 5.3L ECSB 2WD T56:
T76 turbo, Meth injection, 72# injectors, 799 heads, 212/212 114LSA cam, Built 4L80E, 3.42's
EFILive V1 Commercial, COS5 2-bar SOLSD, AEM wideband
Do you know if the PCM thinks the clutch is depressed or released? For my LS1B PCM there were some transmission state pids that would give the info on the clutch, forgot which one though. Mine thought the clutch was depressed the whole time.
2001 Silverado 5.3L ECSB 2WD T56:
T76 turbo, Meth injection, 72# injectors, 799 heads, 212/212 114LSA cam, Built 4L80E, 3.42's
EFILive V1 Commercial, COS5 2-bar SOLSD, AEM wideband
On my 03 I never had any issues with using the A4 tune with DTCs disabled. I bumped my idle to act as a stall saver for acceleration at traffic lights and that was about it. Suffers from some small drivability issues, slight surge on accel but wbo readings were acceptable.