Hesitation on low-speed acceleration

The misfire is more like to be associated with blown head gasket. Which IMO was due to EGR being carbon clogged, likely for the last 100k, but that’s maybe for another discussion. Once the head gasket starts leaking (incompressible) coolant into cylinders, the pistons struggle to get by Top Dead Centre, and that damper takes the brunt.

how long have you had it, since new?

 

The damper takes the brunt of any rotation variation caused by any sort of misfiring at all for any reason.

The accumulation of incompressible coolant in the cylinders makes for a much more dramatic condition, the brunt of which gets taken by the connecting rods, pistons, and sides of the engine block.

You mentioned cleaning the EGR cooler. Was the intake manifold taken off to have its four small EGR passages thoroughly cleaned at the same time?

If those passages are clogged by different amounts, the unbalanced EGR delivery across the cylinders will be made even worse by upstream cleaning of the cooler.

A situation where the rough running is in the midrange, going away at idle and going away at full load, does tend to suggest an EGR-related issue, as it matches when EGR is used: in the midrange, not at idle, and not at full load.

 

It’s not causing those codes, directly. The codes almost certainly are caused by coolant in cylinders one and two, due in turn to head gasket failure (at the wall between those two cylinders), due in turn to uneven heat, due in turn to the beta-version EGR system Toyota doesn’t talk much about, that ideally needs cleaning every 50k miles.

seller could have added a stop-leak product to the engine coolant too.

 

The P030x codes are for misfires, and coolant in the cylinders can be one way of causing misfires. The other classic things that can cause misfires are improper fuel/air ratio, faulty spark, or bad compression. EGR delivered through differently-clogged manifold passages also can cause misfires.

When an engine is misfiring, there are a lot of possible causes to think about. Whole articles get written about misfire diagnosis (see starting on p. 15 in that link).

Sometimes there are clues that help. If there is some misfiring right at start-up, and then it clears up quickly, that might tip the balance more toward coolant dripping into a cylinder overnight while the car was off.

If there is no misfiring at idle, no misfiring at full go, but misfiring in the middle, that can cast suspicion on the small EGR passages in the intake manifold, because that pattern fits so well with when EGR is and isn't in use.

 

I did my EGR system and intake, throttle body around 184k. EGR rad was pretty much 100% clogged any only got it about 90% unclogged. Intake ports were about 1/4 to 1/3rd the size they were supposed to be. I used to have to punch it just to accelerate normally. After doing all this, I would peel out the wheels trying to accelerate like that. Had to relearn how to drive the car. I'm not sure if it has that much power still, unfortunately.

 

I had white smoke, but my mechanic found that because I did not see it. I noticed my radiator fluid level dropped, and just filled it. I did think while my head gasket repair was being done that maybe If I had reacted quick enough to an overheat light that maybe my head gasket would not have messed up, and maybe I missed making sure that there was enough fluid in both the return bottle and the radiator
HOWEVER, many mechanics that work on Prius know that head gasket failure happens alot.
I wish that I had time and moxy to take apart the whole intake system like you did(there is a humerous utube video for a gen 3 take apart and overnight clean soak in brake cleaner) But my method has been intake, engine, and exhaust cleaner repeatedly to keep it at bay.
I would suggest a good Bars/Leaks additive to the radiator fluid just to see if it makes a difference. I have stopped an oil leak at my oil pan gasket and oil pressure sending unit by adding a two part Bars/Leaks made to stop such leaks. 700 miles on the highway and the mobil 0W 40 oil level is holding.
I still have a few misfire codes, but they are occasional, I cancel them and they sometimes come back.
In general, I'm having more trouble with my hybrid battery not holding a charge for very long. It holds plenty of charge as long as the system is warm. And as long as I use it again while it's still warm after a few hours then it's still holding charges.
That's normal also, and I plan to replace the battery with a nexcell LiFeP04 in a few months.
Hope radiator sealers take care of your problem. If not try Dura Lube exhaust cleaner, CataClean, Bars/Leaks two part, Techron, Chemtool, and especially Regain that have a high amount of PEA. I have used them all over the last two years.
HOWEVER, it does seem to have made much more difference to have put Bars/Leaks two part in my oil.....less blowby maybe?

 

I wouldn’t.