Can someone tell me what the difference is between the auto and manual efi harness for the TT? I just recently replaced my auto efi harness and now decided I am going to do a manual swap. My question is why is there a different harness and ecu if none of the wires on the ecu go to the tranny? Can I use my auto ecu and efi harness with the swap?

The auto harness can be used for the manual swap, you'll just have some extra connectors.

But I don't remember disconnecting or connecting anything to the tranny when I replaced the efi harness. Maybe the connectors came off the fuse box? I was planning on doing a JWT ecu upgrade, will I need a manual ecu for the swap or will the auto work?