yea, fluids were all fine.

 

Next thing I would check is to unplug the transmission harness and inspect the pins for any corrosion, also disassemble the shifter MM switches and spray them out with contact cleaner. Look for any possible damaged wiring from the engine swap, the transmission harness does run around the bellhousing and all that stuff got unbolted during the engine swap, it's also possible they REMOVED the transmission to do the engine swap and something may have been pinched or a pin bent in the harness.

Also OBD2 scan again to see if the U1000 code cleared.

Just to verify I understand this correctly, it shifts and runs find in normal drive shifter position, but in MM mode it will automatically shift the transmission anytime the rpm hits 5k yes?

 

The car shifts fine when In drive and also in MM but when I give the car full throttle, it will downshift to 3rd and stay there in MM mode until I put it back over to drive or of course bring the Rpms down to get into 2nd.

 

I'm confused. That doesn't sound like: Everytime I downshift or get near 5k rpm, it forcefully shifts to the next gear and it never did that before.