Hi,
Still sticks in my mind the scanner like Snap On will do you some good. I am not sure how much you get into the engine, but with some of the problems you are having seems like the Injectors can cause some issues. Have you ever put a can of Sea Foam in your gas tank and ran it? I do it every so often, it has kept the injectors clean. I have a set up " an older GM fuel rail that I use to check the injectors " I have pulled all my injectors out and put them on the fuel rail and individually tested each fuel injector for the spraying. I have a solution I obtained off the internet I used to clean the injectors.
Missing when not wet, I would feel takes away the plug wires and such. The car being a 2006 so it is a series III, same as mine then. Bad fuel, crap in the fuel all can cause the fuel injectors to act up. I had to replace all my fuel injectors on my 2004 GTP as it sat for awhile and the injectors gummed up and I could not even clean them out. Luckily the injectors on the Supercharged 3800 are easy to get to and change.
Hope you get to the bottom of the problem soon as I am sure you are getting Tired of wondering what the problem is.