Your post is quite confusing since you state the engine is stock but are tuning MAF and VE tables, why I do not know.

There is zero reason with stock engine to be doing so.

I'd suggest go back to stock setting for those functions.
Set IFR to vales that would be close which is about 25% higher values then stock values are and set PE/RPM values across the table at 1.145

Do the flashing. clear any error codes, do idle relearn, drive about 30 miles for PCM to relearn and then do a testrun with a scanner recording.
From that data tweak the IFR to get LTFTs +/- 5% and only then tweak PE/RPM values.

From what I see in your post is your jumping all over the place and making one area better but then hosing that with changes that are not needed for the PCM will readjust and once LTFTs are close PCM will adjust properly and tune will be fine.
I suspect what you read on other forums has you chasing your tail.

MAF sensors measure airMASS, even if so called porting is done that does NOT change the sensors measuring ablity one bit.

VE as I have shown are for startup and decel under 4,000 RPMs and as a backup if MAF was to fail, THAT IS IT, so screwing with those tables only forces PCM to calculate functions like torque, engine load, airmass, etc incorrectly and thus adjust incorrectly.