From what I understand our cylinder head and exhaust manifold are integrated, and the turbo mounting flange is special to VW only. This means that the most cost effective way would be to custom fab up an adapter to go from the VW flange to a standard T3 flange. The only issue is engine bay clearance. Expensive way would be to custom fab up a new cylinder head that allows a traditional style exhaust manifold.
Other issues include that the turbo set-up is water and oil cooled, so turbo choice isn't necessarily limited, but certainly poses more feed and drain line fabrication. It not only needs to feed and drain oil, it also needs to feed and drain coolant. That, or you could fab up a coolant bypass line that would bypass (whoa) the turbo and go straight from feed fitting to drain fitting.
Tuning is another issue, because AFAIK APR is the only company who has cracked the ECU Protectant Code. It's not as simple as connecting a laptop to the OBD-II port anymore (AFAIK). So, after you put on the new turbocharger that you had to custom fabricate everything for, the car wouldn't run right with the stock computer. This means you might have to call up a company like Haltech to give you a nice tunable ECU that'll work with your sensors.
Now, I've heard rumors that the 292hp 2.0TSI EA888 Turbocharger fits on our cars, but no one has done it AFAIK. Again, the tuning issue is what causes a problem. If your car would need a custom ECU Flash, there's no telling that someone would be willing to do it for you on the stock computer.
Also, I know the MT 1.8's don't have a TCU, but I'm not too sure about the 5 Speed A/T's either, so again another barrier.
In my opinion I would get all of the available tuning. This means APR Stage 2 Tune, Aftermarket Intake, APR Downpipe, 3" TBE, Turbo Muffler Delete, Better Intercooler, Aftermarket Intercooler Piping, Aftermarket Engine Mounts to get most power to the ground, and if that's not enough consider water-methanol injection.
Disclaimer: Everything I've said is on a AFAIK basis. I'm not promising any claims I've made, but just things that I've heard or learned from researching myself.
Edit:
http://www.uspmotorsports.com/Volks...-Induction/Turbo-Kits/IHI-IS38-Turbo-Kit.html I found this.