2012 prius v still has rattle sometimes after 2 engine swaps

Hi everyone,long post but I need help, I have a 2012 prius v that had a blown headgasket and was driven for a long time with it, I replaced the motor myself with jdm one, had a rattle at start and vibration while driving at higher speeds. Ended up replacing the catalytic converter, replaced engine mount and front, rear transmission mounts, water pump,pcv valve after I got a 2nd motor because I thought the first one might have been the problem, still has the same rattle at startup, so I replaced the transmission fluid that was black and smelt burnt, seems to do it a little less often, recently when the car starts on its own in park it makes vibrating noise sometimes maybe once a day that stops when put in drive, my main question is do you guys think I should swap the transmission, im more than willing to do the work just want a 2nd opinion