At wot, the maf should never flat-line.
If your accelerating, more air is passing past the maf as the rpm's increase (Think an air pump that's spinning faster). When you shift to the next gear, rpm's decrease causing less flow across the maf. My 'over-thinking' comes in when I try and understand how the maf knows how 'dense' the air is (Boosted, pressurized).
If your maf flat lines, it could mean you are 'pegging' it at max. That would mean you need a different maf and/or maf tube.
Once you have the software you will be able to sort out the timing. I know there are tricks (That I do not know) to tuning turbo that makes your life much easier. Question is, how do you find out the tricks without living the pain?