I gained the courage to give it another go, after a few failed attempts at VE tuning. I mainly tuned out EGR/AIR, CAGS/VATS, COT, etc and then did the VE under 4k. After the VE I logged MAF vs STFT and just did paste special multiply by 1/2 percent, it barely made any change at all in the graph though. Here's a log and the tune that I thought was pretty much all done, before this I had knock only in low rpm high load cells so I pulled a few degrees there, but now I have more showing up all over. I don't see any pattern as to where and when it pulls timing. Also the STFT's are back positive on this log, they were staying closer to 0 before.

2000 Trans Am
-6 speed swap
-cold air kit/lid/ported tb/ls6 intake manifold
-ebay longtube headers
-tsp catted Y
-magnaflow catback

It feels pretty strong, throttle response is much better too. Any comments or input on the knock or other tweaks?