As far as engine mount at back of the engine, you're not going to be able to use the stock MK2 or MK3 mount if you want to keep the turbo - I have a vnt turbo and I bought a steel mount online here to the turbo outlet will clear the motor mount. I'm not sure what your tdi has, but I'm thinking you may have to do the same.
As for the rest of the mounts, you should have no problems between the MK2 and 3. The early MK2 and later are the same. My 1.6 td is out of a MK2 86' vintage into a Mk3. everything is the same except the motor mount is a single bolt to the mount on the subframe, where the MK2 has 3 smaller bolts, and the actual mount itself is different as well. you probably already know that if you have a MK3 subframe.