Hi Ethan. The Alt harness should go behind the motor mount bracket, then turn up the side of the exhaust header. Mine is a TT, but I can show you a pic that I took. There should be a bracket that mounts in front of the header and heat shield. The Alt harness clips to that with one of those round harness clips. That should keep it from touching the heat shield.
Here is the pic, it's small because I loaded them to photobucket. In the pic, the harness is not attached to the bracket. But if you look at the bracket, you can see the remainder of a black clip that broke. It attaches to the bracket through a hole in the bracket and then clips around the harness to keep it steady.
I hope this helps...
Marty