Aight...  to kind of introduce myself, i've lurked and learned LOTS of stuff over the past year or so with things besides actual tuning.  A close friend of mine has a '01 GTI, AFP 12v VRT, 5 speed.  he did a moderately budget minded build on it with a T3/T04e.  Its got all necessary maintenance and such done, so none of that should be an issue.  WOT it spools pretty nicely by about 3k rpm.  running 8-10 psi.  It currently has software on it from a popular tuner that sells their work via social media.  i'll refrain from naming unless necessary.  To put it politely, it runs like garbage, and the tuner doesnt seem to want to support it...  My mission: write a proper tune for it so that it runs like its supposed to. 

i found a proper stock file and xdf here, and thats what ive used so far:
http://nefariousmotorsports.com/forum/index.php?topic=4620.0

I have the demo version of Winols, but would prefer not to use it if possible, as i'm far more familliar with Tuner Pro. 

i was able to set KRKTE via "cheat number" to what seems to be pretty close to necessary for his injectors.  440's @ 4bar. 

i also did some work to MLHFM to try and get the MAF readings proper. I first tried to scale it using mafadjust, from the stock 70mm ID (best of my measurable ability) to a 83mm ID 2.7t MAF housing.  it ran OK (no boost), but not quite like it should.  CFM readings seemed to be exceedingly high for the given RPM range, and the MAF would exceed range and shut off with any more than about 4k rpm (again no boost) so i just started taking stabs into the dark for scaling, with little to no luck.  i then tried to scale it to the 4" MAF housing and stock sensor that he's been using.  scaled from 70 to 96mm, and it ran mediocre, but very rich.  On a whim despite knowing it would probably be WAY off, we stuck the 2.7t's sensor (Bosch) in the 4" housing, didnt change MAF table, and it idles properly at about 14-15:1 AFR...  it actually ran quite nicely overall and had decent low rpm/load/boost drivability.  light pedal input and low boost, like a lb or two, it would stay around 13:1-ish, which seemed acceptable all things considered.  but... high rpm it would still exceeded MAF range and kick off the MAF, and confuse everything.  one major hiccup with that particular setup was that ignition timing seemed to be a good bit off as well, but i dont remember what the readings were.  Timing tables have not been touched.  i want to get MAF and fueling proper before i poke at timing, etc. 

so...  Here's where im asking for help...  if someone could give me some insight as to what i might be doing wrong, MAF scaling or otherwise, as well as some suggestions on what else would benefit from changes.  Also, the definitions dont seem to be right on a few things. the tables are there, but the locations seem to be incorrect. 

i've read a lot, but not everything, and im not completely clueless as to what i'm doing.  ive just not come across any other posts with something similar for me to go by and get a good "running go" with.  plus missing a few critical tables is hindering progression. 

if things attach like i expect, you'll find my various bin's, the changelog of whats what, and my xdf. 

Again, please keep in mind that this is my first time ever to poke at values and stuff it in a car...  Starting with what I assume is a stock file.

I don't have any logs yet. I have legit VCDS, but my laptop is currently unavailable. I've been adjusting with TunerPro, and flashing with my desktop, bench harness, and MPPS. The info we've watched so far has been from a wideband AFR gauge, and a OBD2 Android app the car's owner has set up, I wanna say it's Torque...??  Maybe...

I am perfectly content with using the S4 MAF. I tried to find a 2.7t file to pull the MAF table from in the first place, but didn't have any luck with anything that had definitions I could read. It likely exists, I just couldn't find it...

"Please get rid of some timing..." I appreciate the input, but more information than that would be appreciated. Again, this is my first time, and the xdf doesn't seem to be fully defined, so I don't know if offsets and all for various things are even correct.

Listen to what Marty said, ME7logger will be your friend. I honestly can tell you I could not take you the full distance
with this file as it will be above my paygrade but there is alot of good info and good people here that could. My intenet was
to get you going on the right track so someone else could step in a help. 
When I said get rid of some timing I meant pretty much just that I dont know how much (again Logging) but leaning on the knock
sensor to keep your motor from blowing up is not a good move. Since we are still messing with the maf have you relocated the IAT
to somewhere after the intercooler? this will help with timing and is often over looked by even the best tuners.

You have the source code and a compiler?

You *might* be able to compile snippets of c into asm, but you'll still have to had patch stuff in, and probably do tweaks to the resulting code.

i speak computer, my day job is an IT guy, but that stuff is above my head.