2009 Power Wagon has multiple and changing check engine codes after a rebuild install, does the PCM need to be flashed?

[DINGO04]

My 2009 Power Wagon had a cam lifter failure at 214,000 miles. I installed a rebuilt engine, and I now have random and changing engine codes after every startup. I have new coil packs all new sensors, double and triple check all the connections. The PCM and the TIPM are also new installed by a local Dodge dealership. I can start the truck without any codes coming on, and it'll stay that way for a day or two or a few minutes. My question is does the PCM need to be flashed? Thank you for you help