You can use a mk3 or mk4 pedal, but the mk3 is the easier one to use, the mk3 pedal is very versatile, can be used externally, removing the short cable attached to the quadrant, and either make a mounting bracket, or buy one, and then use a normal throttle cable with a solderless nipple to operate the quadrant, this is the method I used on my PD B3 passat. ALH wastegate turbos do not hang down as far as the vnt turbo you are thinking about, just look at a B4 1z and you will see what I mean, it's more or less the same turbo.
Yes the plug I changed to the 10 pin was on the original wiring loom with a 028906021xx ECU