Update:
After a few weeks of being out of town on business I finally got it in.
The noise from the roof ended up being the (HVAC) -temp sensor- and was a easy fix.
The Nav unit was fried. They had to order me a new one and will be doing all the work for free. Dealer said this is the first time they've ever dealt with that message ("over- heated, shutting down") or this problem before. In all they fixed it all no problems asked.
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