Rebuilt transmission in 95 GMC 2500 Sierra, and it still on some days not shift

What is your question?

I have had a 95 GMC in the shop for 4 months and it still running the same. Had rebuilt transmission, replaced TPS sensor, reground all wires, replaced 4 wire harnesses, replaced Alt. The problem is Once in awhile the Check Engine light comes on and the truck wont shift into 3rd gear, unless I park the truck and wait a few minutes and restarted it. Any Idea's what this "Gremlin" is?