You've probably cleaned all the grounds but that is always a good thing to do. The manual has some checks you can do on the MPEM but I find those checks can be misleading. I had the same readings on two MPEMs and one worked, the other didn't. I had an issue on a 1996 GTI where it gave me trouble starting, then after starting it would not shut off. Ended up being one of the larger flat terminals on the MPEM that needed cleaning. I'd check the wires at the MPEM plugs.
I also had trouble with my GTX and when I began pullling the connectors apart I found dirt in one. Just gotta stick with it. They get weird. Good Luck !!