1998 Dodge Ram Shaking and exhaust

So we changed motors. We got one from a Salvage yard because it was cheaper than doing the head. Hubby is gonna rebuild the motor that was in there when we have the extra money. (It was just him and I doing this work and it took us 3 days with everything that can go wrong doing so. NEVER do I want to do this crap again. Just not my cup of tea!)
Now with that said we have to change the O2 sensors. They are throwing codes.
The transmission is loosing fluid, we are not sure from where. We suspect the transmission fill tube since the piece that is supposed to be there to bolt it to the engine broke off. We don't know if it jolts it when it is driving and causes it to spill out. With all the rain we are having he can't get under there to see if he can spot the leak. We refilled it yesterday and now the tranny will not shift into 4th gear. On his way to work he focused on the tranny shifting this morning. It shifts into 1st, 2nd, and 3rd just fine but won't shift into 4th.
It was fine before and it worked after we changed the engine. We are adding ATF+4 which is called for, for our Dodge tranny.
So could it be a sensor in the tranny or even the O2 sensors causing it. The code reader did not detect any tranny codes when he had it read just both O2 sensor codes. I have read that it could be the linkage or even the governor sensor & solenoid.

Changed the O2 sensors, now it is throwing 2 TPS codes. P0123 and p0121. We changed the TPS when we put in the new engine (7 days old today!) And changed the IAC yesterday.
Hoping to scrape up the money to have to put back on the machine since it is still throwing the codes. The truck won't shift into 4th, the cruise control will not engage, and the truck is seriously burning fuel. I called a shop and they said if the IAC is not bad it is something with the computer. I am beginning to hate this truck!

Oh and we found the leak. It is the dipstick tube. He has to get it bolted. Since the piece that you bolt to the engine broke it is moving too much, allowing fluid to escape where it goes it. He discovered this while putting in the new O2 sensors.