Engine shakes while charging hybrid battery

Well.. i put a 30k mile engine from a 2020 prius with the clutch/dampener pack along with it. Just thought id have to ask it came from a prius prime 2020. I had it put in my 2016 prius two... i had a bad head gasket issues with heat exchanger on the old engine.

Although I have excessive exhaust leaks bad at the heat exchanger, im going to be changing out the front pipe catalytic converter assembly next week hopefully.. plus new engine/transmission mounts when they come in the mail. I will also be taking the egr valve off to check it for deposits inside and checking the crank sensor as well and clean as needed if it's dirty.

I changed out the maf sensor as it was malfunctioning had 385k miles on it. Cel for it went away afterwards.

I also changed out the oxygen sensor on front pipe assembly as the cel light for it was on and both the oxygen sensor/maf were confusing the computer with slow change or speed of change in fuel ratio rich to lean or vise versa. Cel light for it went away after replacing. The old sensor was obviously contaminated from head gasket issues and or worn out due to mileage.

Ran great for a few month or so and now im noticing engine shakes while charging the hybrid battery when its low, shakes the whole car and I feel it.

I even checked the plugs they all look great, no problems there. It was the first thing I looked at as I felt like it was possibly misfiring. I did eventually get a cel light fir misfire in all cylinders but it eventually went away.

The shaking happens when the car is in park mode and engine is trying to charge the hybrid battery. If I put it in gear and or drive, it's fine, no issue.

Any advice what else to look at or check out?

Thank you