Couple things.
Please add the 'MAF status' channel, it will indicate if the MAF is failed in real time.
Do not log MAF channels when failing the MAF (Mass Airflow (why more than one?), MAF Sensor Hz). Cylinder Airmass is not a MAF reading, keep that one no matter what.
After flashing, start the engine, let it idle a few seconds, then shut it off and then restart and then begin your log (or, run until up to temp then start log). Sometimes the MAF DTC(s) will not show up if you start logging on the very first run cycle after a reflash. It can still be in SD without the DTCs visible in that first run cycle, it's just another data point to let you know it really truly is doing what you want it to do.
Let's say you have it tuned with stock injectors. If you then replace with larger injectors, and input all the data correctly, theoretically, the PCM should not need to be retuned to remain in the same state it was before. Theoretically. No data conversion is exactly perfect so there will be some skew, but the closer the injector data is the closer the old VE/MAF tables will be after the swap. I have to point out that your injector data is rather different than what I have for the L96/12613412s in P59 format. I feel like we have been over this before...
Short pulse adder, yours:
yours.png
Short pulse adder, my conversion:
mine.png
Short pulse adder, original L96/E38 data:
L96 source.png
Can you just try it with this injector data swapped in and see what happens? Please?
reset and retry - 2nd round SD - towing adj 3 - added 3p to ve - 12613412.hpt