The saga continues....
2004 f150 4r75e

Long story short, I hit a rock, dented the pan, took out the solenoids, broke the tailshaft. Got a new pan, replaced the solenoids, put a new tailshaft housing on. Test drove it and it acts like it slips then catch's, and the malfunction message still comes back. Does the computer store the malfunction and go into some kind of "limp" mode...If it does. by pulling the neg terminal for 20~ minutes clear the computer?

 

Yes... but it sounds like the transmission is having an accute symptom of trying to self-destruct.

 

did you check the lead frame harness that is inside the pan that connects to all of the solenoids when you did the repair ?

 

The OD light will only flash if the problem it sees is still there. It won't flash for an old code that is stored in memory. You are going to have to read the codes to see what the computer is seeing. Then you'll know where to look for the problem.