Electronic shift problem or Tranny?

I am having problems with my 2003 F250.  It is a 6.0 diesel, auto, 4x4.  I started out having wiring problems that ended up being my junction box.  It is a builder that I have replaced the whole left side sheet metal.  I have put an instrument cluster in also. I did some welding on the frame and body and thought that I burnt up the instrument cluster but it ended up being the junction box.  Well, it is all done now and I took it for a drive and now when it shifts, oh probably out of second into third it shifts out of gear like I threw it into neutral and the overdrive off lite on the shifter starts flashing, then if you wait a second it downshifts and takes off again, but the light just flashes on and off.  Any advise would be greatly apppreciated!!!  Spent $1000 the last week trying to get this thing on the road, just about ready to throw a match in it.

Also put a used rear end in at the beginning of project, the old rear end was bent in accident.  Could this be a speed sensor in the rear end and how can i check that by myself or do i need a scanner