I guess I'll post this in the open for all to see...

I have had little experience with thermal pads, other than removing old and/or contaminated one which can no longer serve their function.

Specifically pertaining to the Mac Pro GPU, I used thermal paste. It seems to be working just fine. You could try a pad; I don't see why it wouldn't work as well.

Just a parting tip when disassembling the heatsink: be careful! It's kind of tricky because of the way it's attached to the PCB (although that could've been due to my lack of experience).

Good luck!!

c