Need help on VVT AFM disable

A buddy of mine has a 2012 Silverado with a 5.3 that had both AFM and VVT. He swapped in, I think, an LS2 cam and associated components. He had me shut off all the stuff related to that in the tune, but now he is throwing lean codes. I suspect it is because the new cam is moving more air, and the injectors are compensating so much that the trims are going lean trying to keep it in line. I've never really played around much with gas stuff much, and never an E38 ECM. Can anyone point me to a thread or give me some advice on how to fix this? Thanks.