Are you experiencing any other weird electrical problems? Check for dampness in your carpet, especially the passenger's side next to the kick panel. Pull it back and see if you feel any moisture. Some Mustangs have experienced problems with leaking thus creating havoc on the electrical systems.
If that's not it, send 157db a pm.....he is the electrical guru in this forum.

 

No water I sealed that area off a long time ago

 

The SJB does not control the windows functions.
The logic boards are on the motors themselves.
So forget about a water leak SJB problem.
If the express works from one door but not the other,
I would suspect a bad switch on the door that the
express function does not work or a broken wire
from the drivers door to the passengers side door switch.
Click link for the wiring diagram for the windows.

 

well my alternator was screwing up earlier but then stopped maybe that screwed something up since the diodes in it were bad

 

Yep, the system does not like the AC ripple from bad diodes.
(if they shorted closed)