I would have expected to see more than 32 LB/min peak in a pro charged coyote. another 1000RPMS and youd be at the max of your MAF curve. I think your SD changes are causing you to tune your MAF curve wrong. With your MAF that far off your torque values and load values would be too. That or you have your MAF in a very small pipe.
MAP max delta above BP, you are over twice what you really see. calculated MAP max you are about a third too high. MAX load is too high. Load at WOT is stock(about half of max load). These things can cause your MAF value to be wrong when the cylair filter is enabled.
Then you have OP enrichment required disabled under your VCT. This basically makes fuel enrichment based on pedal position and desired torque for load, which you are probably around half or less of what you should be from the MAF values you are seeing.
I'm surprised lowering your max torque values did anything at all.