As you know, the A4ld is a ticking time bomb with anything more than about 180-200 hp a the crank. At least I killed two or three of them that way.
Yup, your T5 cross member and driveshaft should work. You'll need a C4 trans, bell housing, torque converter and flex plate. Your T5 would have a block plate, right? If not, you'll need one of those too. You can buy a stock replacement converter. Do a search over at turboford to find the right part number. You'll want a converter with the 2500 rpm stall (if you aren't having one custom made for an even higher stall). You should to add a vacuum line to the modulator valve so it knows how to shift automatically, but a check valve with a small bleed hole after that would protect the modulator valve from seeing boost (and breaking the seal on the valve). That happen to me a few times, but that was closer to 20psi. You may also want to add a kickdown cable, but I never did.
As for which trans, any case fill transmission should work well. There were lots and lots of cars that came with this trans. I suggest a V8 car as they supposedly got an extra clutch? and better servos? Something was different anyway. I would just suggest a simple shift kit. That will make the shifts quicker and more firm and allow the trans to hold more power. With a shift kit, an otherwise stock C4 will hold 300 rwhp all day long, year after year. That's what I ran in my 88 mustang.... rebuilt C4 with a shift kit and stock converter. I sprayed it off the line too many times to count, and went quick as 1.6 60' times, on to 12.2's at~110mph.