Well I cleaned up all my battery connections and shock tower ground, and I have power back in my system, but it still goes haywire when I try to start it. Guessing my issue is with the starter ground now. I'm going to buy some jack stands tomorrow, clean up that connection and see where that puts me.
I'm just glad I got my window controls back and was able to roll them up! Week's forecast here in Michigan, 100% rain. Joy.
However, I'm still worried about this passenger side leak into the smart junction box I've found all over the internet for the 2005. Car's working one day, it rains, system no longer works. Ford charges over $1000, and still doesn't fix the issue. Not a scenario I'd like to see.
2005 Mustang GT - C & L Cold Air Intake, Flowmaster Exhaust