2006 Dodge Ram 1500, 4.7l 4x4. This truck has a new engine, installed by myself, and a new PCM installed at a Chrysler dealership. Since the new engine and PCM, the Automatic Transmission doesn't want to shift to 3rd. I thought maybe the linkage was off or something, but N is Neutral, 1 is 1, 2 is 2, Drive is 2. I can jiggle the gearshift while driving and it still will not shift. RPMS just keep climbing, I back off before they get to 6000. After the Engine was installed, when I first started it, I let the truck warm up for like 20 minutes, and I then drove it down the highway with no problems, It shifted all the way to OD, nice solid shifts. Ever since then it won't shift past 2nd and I can't get it to throw a code for the life of me! Before the engine swap, I butchered the wiring harness, had to rewire 5v supply for MAP, Camshaft sensors, and EGR Valve. Is a transmission control wired in with these? It's the yellow/lightpink wire in the harness that I bypassed due to a short. Maybe it's a solenoid? How can I check? Any help is appreciated. Thanks!

Update: If, while driving in 2nd around 45mph, I drop the truck to neutral then immediately back to drive, it will shift to 3rd. After doing this about 3 times while driving through town, the truck will shift normally. So, once the truck is warmed up, it shifts correctly. But when it's cold, it won't shift past 2nd, unless I put it in neutral then back to drive while driving in second gear.