When I did mine, I switched the tip harness in and the manual harness out. The tip harness has a whole nother circuit for the transmission, and another connector in the trunk. And the vacuum and the coolant lines are different.
What would I do? I'd swap the stuff over to the new engine. It's extra work, but you'll know that the wiring is all okay. You can delete the coolant lines and use the 3 way splitter in the vacuum lines. Do all that while the engine is on the stand or a furniture dolly. Not too bad.
Hey Brian:
I think you may know the answer to a question I have: I am replacing the engine in my 2002 986 base (manual trans) with an engine from a 2000 tiptronic car. I know that the wiring harness for the tip engine might have some added features that the manual harness does not but is there any reason that the tip harness won't work in a manual car? I am trying to avoid a little extra work by having to switch out the harnesses.
Thanks!