Q: Transmission issues, slips from second to fourth gear

Hi, I have GM problems that I'm having a difficult time solving. I have a 2001 Chevy silverado 1500 with a 5.3 Vortec. I had the transmission rebuilt and put it in, it shifts through all gears but slips 2nd to 4th under normal acceleration. I have a crp 123 that I hooked up to the truck and these are the codes it's giving me. U1041,U1016,U1096,U1064 Any ideas where to start or where the problem is at? I've checked the ground wires on the back of the block, took off the old braided copper wire, put on new wire, there is 2 ground wires on the same bolt. I'm stuck, what do I do? I've changed the computer with the exact match, and the truck starts and dies. If I put the old computer in it starts and runs but I have these problems as I've described above. On the red connector on the computer, is there supposed to be any wires that have wires spliced into them? I had 2 wires that were spliced into 2 wires on the red connector and I have no idea what they are for.

My car has 210000 miles.
My car has an automatic transmission.