I have a SN95 that's been coyote swapped, only modifications are a cold air intake, long tube headers, and an IMRC delete. The car came to my shop because it hadn't been tuned by the installers of the engine, and it had a throttle surging problem at part-throttle, from anywhere between 1500rpm and 4500rpm, with IPC torque error spiking in conjunction with the surges. I've been making adjustments to my torque and inverse torque tables to eliminate my throttle angle error, and have done so successfully, as my initial errors were over 10% in some areas (despite having a stock throttle body) and now are less than 1% for the most part, with no improvement to my IPC torque error spikes but considerably less surging. However, now whenever I go to do a log, as soon as I get into second gear between 3500-4000rpm, my torque source switches from driver demand to ETC FMEM, it completely kills power delivery, and my IPC torque error pegs itself at seemingly random high values. My throttle angle source also switches to FMEM - throttle follower and my spark source also switches to torque control. I see no indication as to what could be causing this to happen. The first time it happened, I had not adjusted any driver demand tables, but before the second run I updated the DD tables to match what The Tuning School suggests in their "Ford Coyote Engine" tuning course textbook, to no effect. My engine brake torque is mostly always exceeding my desired brake torque and ETC torque request, but only by 20-50ftlbs, despite having reduced the stock torque tables by a good amount to accommodate the throttle angle errors. I have in the process also been making MAF adjustments, but my short term fuel trims are reasonable the whole time, and I have very little spark retard. I know the throttle body, MAF sensor, and accelerator pedal position sensor are in proper working order, and their harnesses are undamaged. If it makes any difference, the car has the stock SN95 five speed manual, so the ECU is a Ford Performance standalone that receives no data from the transmission. I'm struggling to come up with anything to resolve this, so any help would be greatly appreciated.

I've got my current tune here, as well as 4 logs displaying what I'm dealing with, two separate instances of the ETC FMEM error, my last log before this occurred, and my initial throttle oscillation/surging log.

96mustang_log9_etc_fmem.hpl96mustang_log8.hpl96mustang_log7.hpl96mustang_throttle_oscillation.hpl96mustangcoyoteswap_rev10.hpt