Idle issue after Gen3->Gen4 engine swap

Hello,

I recently did the engine swap procedure on my 2011 Prius. The car runs and drives, but when idling or pressing the gas pedal when in P the idle is unstable (it sounds like you're lightly tapping the gas pedal repeatedly).
When driving, I didn't notice this behaviour flooring the gas or under normal acceleration, but the engine is pretty quiet when normally accelerating anyway.

The engine was taken from a 2016 XW50 and the engine code on it is X2ZR-Y22. The mechanic also had to replace the thermostat housing with a 16331-37100, because the one on the new engine didn't fit.

As far as I know, they reused everything from the old engine, including the EGR. Or at least I pretty clearly told them to.

What would be the cause of this issue? How to fix it? Is driving the car like this a stupid idea, or just a minor annoyance?

 

Would that be the cause? As far as I know, they modified the Gen3 EGR and installed it.

I know that using the Gen4 EGR can cause problems, but I didn't find anything actually detailing what kind beyond the vague claim of "driveability issues".

 

Funny that you mentioned this, because there were a multitude of issues with the shop, and the whole process took around three months because of that.

I should probably mention that there was a transmission issue (DTC C2303) which another mechanic managed to fix by straightening some pins to my understanding.

Anyways, for whatever reason, the hybrid battery actually got discharged during the engine swap and the car didn't start even after fixing the transmission. They charged the cells and it starts now, this being the only problem that remains.

I'm interested if the car is drivable like this without causing permanent damage, while I try to sort out this problem because in the long run it probably won'g be good, even if it was a minor issue.