I sit possible that you've missed a ground wire on the back of the intake? I know on Toyota 3.0 and 3.3 engines, there are 2 or 3 combo grounds that you can't see from the front side.
Have you tried following the harness for the cruise and just checking things out? Also get it up on stands, crawl under it and just take a look. Not at anything in particular, but everything. I can't tell you how many things I've found wrong with various vehicles simply by looking around from underneath, as the view is usually pretty good.