Sounds like you are on your way to finding the solution.

I just changed out my cabin filter and cleaned out the drain. It definitely was needed.

 

If I'm not mistaken, the SJB is attached with only a single bolt at the bottom. If you Google "Mustang Smart Junction Box" there are plenty of images. Inside the box is a circuit board.

I wish I could answer your questions about the symptoms a wet box will cause. Mine has not got wet yet so I can't say. What I can say is that it controls a great deal of functions in your car and a wet passengers floor leads me to believe it's the likely culprit.

You can get an OEM new off eBay for $280. This one is for a coupe:

http://www.ebay.com/itm/like/321540702794?lpid=82
However, having not replaced one myself, I don't know if Ford needs to program it. You might want to check with them first to see if the symptoms you are experiencing could be from water infiltration.

 

Anything that deals with PATS should be taken to FOrd to resynch.

That being said, replace the SJB first, then see if the car continues to have the issue. At worst, take it to a dealer to troubleshoot and actually find the problem, then just take it back home yourself to fix. At most it will cost you a couple of hours of diagnostic. It beats the heck out of throwing parts and more $ at it.

I do that sometimes if I get lazy, don't have the time, or the expertise to find the problem. THe mechanical side of cars (replacing stuff or rebuilding stuff) is easy. It's the finding out what the problem is that can be hair pulling sometimes.