We've had our share of bad experiences with the AFC.
I can tell you from personal experience that you can't control your 36lb injectors with that tuning. Nor can you outflow the stock 29lb injectors the engine came with, nor can you even control THEM with the stock trofeo coding.
What MAF sensor are you running?
What exhaust manifolds are you running? Modified? Stock?
What did you do to the LIM?
What specifically did you do to the supercharger?
What FPR are you running?
To my knowledge, I'm the only person to have succesfully run a 2.0" pulley on a Gen3 M62, and I'm still on 29lb injectors with perfect fuel trims. And I can bet you that my top end flows alot more than yours. In fact, I'm improving that again right now.
Your biggest problem is the stock Trofeo PCM. You will get nowhere with that. If you're set on using it, you need to go back to at LEAST a 2.55" pulley, but probably more practical a 2.85" stock pulley for that Gen3 setup.
Did you upgrade your FPR and fuel pump?
I suspect your injectors are drooling instead of spraying efficiently. Because they're 36lb injectors AND the possibility of you not flowing enough supply flow and pressure to them, in spite of the fact that your Trofeo PCM doesn't know how to control them.