I have a mk5 GTI 2.0t FSI 6mt. 200k miles, still shifts like butter, but the FSI is tired (stage 2 most of its life, typical hardware upgrades) and I have no desire to do anything with it any longer, so any suggestion to do anything with the FSI will fall on def ears.  Not being smart, I just don't want to work with that engine.  In the recent past I acquired a '08 Jetta 2.5 (CBT, ME7.1.1) parts car, and was planning to use it for other purposes, but that ended up not happening.  The other day I started thinking about doing a bit of a budget build 2.5t for the mk5 GTI, and was curious if anyone had ever poked at a turbo 07k file, not TTRS. 

Ive done some reading, and I know the 06-07 Beetle ECU is the one to work with out of simplicity's sake.  But...  Ive done some experimenting with a prior project, and I'm 95% sure that mk5 and mk4 throttle pedals arent compatible.  I did a bunch of legwork to see about making a 1.8t work in the same GTI with the 2.5 donor cars wiring, and after taking a quick look at wiring diagrams and a little repining, the 1.8t ECU didnt seem to interpret the mk5's pedal inputs properly.  Although, I may need to do some more poking on that subject to be sure. 

I forget the number on the ecu I have, but I'm 99% sure its a ST10, not Infineon. I wouldn't mind going with a ME17, since it would require very little rewiring in the GTI, but I have nothing to read/write a ME17 ECU, unless a MED9 BDM is compatible.  I'd also have to get a new engine harness, and a few different sensors. 

My thoughts were to maybe look at some maps as found in a stock TTRS file, for ignition and such.  I imagine fuel maps would be different since its direct vs port injection.  But on the subject of making it understand that boost is a thing, i'm clueless. 

Any help and insight would be much appreciated. 

Not sure what the reward is going to be on this. If you want a turbo'd 5 pot, fit a TTRS engine and management. Far cheaper, easier and reliable in the long run than to turbo a 2.5 NA engine and make it work.