So there are two maps that directly correlate to MAF housing changes:

MLHFM, a general map for dictating a particular sensor/housing combination
KFKHFM, a map for dialing in the fine tuning of a particular intake tracts influence on the MAF readings at various load/rpm points

This I fully understand.  What I would like to know however is how you go about extracting the basic MLHFM information when first setting up a new MAF housing without letting your (at this point) untuned KFKHFM map also influence your STFT/LTFT feedback.  For an example, I am using my car, keeping the injection system stock so as to isolate any fuel map influences on STFT/LTFT, and swapping in a 034 billet MAF housing with hitachi sensor.  You keep the stock hitachi MAF signal curve, and just scale it by some constant % offset based on the new housing size, and use feedback from STFT/LTFT to tweak the percentage change.  However, since KFKHFM has not been adjusted yet for my intake setup, how can I ensure that the feedback I am using isn't in some way manipulated by this untuned map?

How close to zero should your LTFTs be when dialing in the MAF housing on stock fueling/fuel maps?  My first attempt at flashing yielded around -5 on bank 1 and -8 on bank 2 at idle and roughly -3 or so at part cruise.

Excuse me if I'm new, but I tried that by firing up VCDS, then going into the engine module, and then basic settings, and the 099. Literally all of this is new to me, but I don't see anywhere that I can turn LTFTs off?  I'm sure I'm way off on something here.

I suggest that you get your injectors dialed in on stock MAF/intake first.

I will 2nd or 3rd the motion of dialing in your injectors first on a stock intake/maf.  I tried to do both injectors and maf and it drove me crazy.  Went back to just getting the injectors settled and it made life simple when I started dialing in my maf