I looked at your scans Ben...there'* some hints in there and a few details missing as you mentioned.
As I expected, despite some needed tweaks, your motor runs fairly well (still need to see the O2s) and without KR while at WOT. We don't see the TCC duty cycle, the O2 or the TPS% while cruising but you can see how the engine load changes with gear changes and TCC lock.
Your MAF is not calibrated correctly, not surprising given your mods. You can see the LTFTs are negative, meaning the PCM is pulling fuel to meet the Target AFR at both WOT and cruise. While at WOT and commanding an 11.6 AFR, the fact the PCM pulls 7% fuel doesn't lead to KR but it does when the engine load is greater in 4th gear with the TCC locked. You can see where you shift 4th gear and then the TC locks and the KR builds quickly, compounding the problem we see the commanded AFR is 14.7 (stoich) and the LTFTs hit -10%...it would be interesting to see the O2s under these conditions.
Changing the TC parameters can have a great effect on the tuning and drivabilty on the highway. In conjunction with your needed MAF tuning, some tranny changes corresponding to engine load and TPS% settings would go a long way to improving your situation.
If you could scan with another program like Autotap that would show O2, TCC Duty and TPS % then we could look more closely. Longer scans would be helpful too, 3,000 lines would be a typical scan