I had a very similar problem and tried everything you did just about. This Ty already had a lot of mods done to it when I got. I ended up replacing everything trying to track it down (o2 sensor, Fuel Pump, Fuel Filter, Alternator, FP Reg., New 3bar MAP, put the Ultimate in there since the guy had a 40 lb chip on stock injectors) but still had the problem. The last thing I remember him also saying was, he had a Prompaq in there at one point. Then I was like crap... Bet you my ECM is bad. Replaced it and now my knock only happens at shifts briefly. So you might want to try that. My ECM showed no signs of being bad at all. All the Datamaster runs looked good, just had knock. Nothing in the Datamaster runs was pointing to the ECM but thought what the heck give it try. Problem fixed.
Now that it is running good, I am getting an overboost. But atleast the knock is gone. It will run 20 psi on the 16 psi ultimate setting with no knock. My WBo2 is also showing 10.5 afr at this point so it would seem to be ok (Little Rich) but the fuel then just cuts out so it is overboosting. So I need to put that spring in the 20g that Dig said would fix that. If it isn't one thing it is another. :-b