I too have a key fob issue. I had three when I bought the truck new. I lost one, seldom used one (my spare), and the third works great. The seldom used one works intermittently. I took it apart, re-centered the metallic discs, cleaned the contacts on the circuit board, installed a new battery and it worked for a few days. Now, if I use it to unlock/lock the doors it sometimes will start the truck. Sometimes I have to re-enter the fob 180-degrees and it will start, and sometimes the dash message says "wrong Fob". I read somewhere on a Forum, if the doors lock and unlock, the fob is communicating with the truck.
If the lock/unlock fob internal discs are off center and making connection, and the battery goes completely dead, does the fob still stay programmed, or does it loose part of the programming? The lock/unlock always works. Are there any operating or troubleshooting instructions in any repair manuals you can share?