Misfire troubleshooting issue

Hello all, I run a small time shop at my home and currently I’m working on a gen 3 Prius 4. Long story short I replaced the engine in this unit with a customer supplied engine from a jdm car. Customer purchased the engine from a place they said was reputable. In the past I’ve done all the maintenance while they owned the vehicle. 2.5 years ago the head gasket was replaced in their old engine and it blew once more. Egr was fully plugged causing this. Now once the engine was in the car we put it in maintenance mode and the engine ran fine with no misfires or codes. Car was driven for 1 day then came back for an engine misfire condition. It was coding for cylinder 3 misfire. We put another new set of plugs in and a set of ignition coils. Car ran okay for a few minutes. Comes back with #3 misfire. We decide to swap fuel injectors with the ones that came with the used engine, still #3 misfire. Triple checked all connections and wires in the harness nothing out of the ordinary. Injectors are pulsing and coils are firing. My prognosis is a blown head gasket between cylinders 2-3. Once you unplug #2 cylinder coil, the engine smooths out. Leading me to believe a combustion leak between the adjoining cylinders. Customer thinks it’s something else. We have not done a compression test or leak down as of yet, we ordered a tool for this. My question is has anyone else has a issue quite like this without a blown gasket? Car smooths out when placed in neutral but there is still a misfire.

 

I was told the engine came out of Florida from a sunshine state jdm company. I’ve never personally talked to these guys. But the car is now coding a p0455 emission control leak detected. (was a loose hose) I’m guessing from the engine moving around with the hard miss. Then is coding for P0441 evaporative emission incorrect purge flow. We replaced the valve new and still setting the code and misfire still exists. I would imagine if this was an issue it would cause a miss on more than one cylinder. Or that it was set by the hose becoming loose.

 

Yes the egr cooler was replaced on the new “used” engine. So I know the cooler is good. I personally cleaned the egr tube and passages in the intake manifold and have triple checked it. I will borescope it and see where that takes me.