I can't speak to the technical parts of the discussion, but at a high level I'd say it sure seems like you might want to go back to a correct/native installation while you're doing all this. Have your guy make sure you have all the right 3.5 parts installed while he's inspecting everything.

You could always buy another engine from a reputable company, but that's a lot of $$$ - seems like trying to fix what you already have is worth the risk.