I am swapping the engine (3.0 quatro automatic) and I ran into some problems during installation of a new one. First I discovered that my harness on the new engine is different from original one: it is missing one connector (orange) at a fuse box, hence I have one extra spot in there. I would like to keep new harness with the new engine. Another problem is that when I mated engine and transmission for some reason alignment pins (two of them) would not go all the way inside transmission bolt holes. I am about to split it again and file down either holes or pins, but if anybody got better ideas I would greatly appreciate it.

 

The 3.0L is such a POS that they probably changed all sorts of crap from one year to the next. I would file the pins to fit. as for the harness you need to find out what that wire goes to and what it controls. Then you'll be able to adapt it to work somehow. Did the old engine have a chain driven cam adjuster and the new one have hydraulic??? I would also chase the old one on the old engine and compare it to the new one. Make sure it didn't somehow get removed on the new engine.

BTW I don't know if this is your personal car or not but If it were your personal car while that engine was out it would be a great time to get to some of the seals and crap that always go bad.