Prius misfire coolant throttle body

Sounds like you need Techstream to try to figure out what you are missing.
You are saying you have confirmed ignition but what about injector pulse a d fuel?
A cylinder leak down test wouldn't be bad either.

 

Look for the threads on EGR cleaning, intake cleaning, and blown head gaskets. Also, there are links up top to "nutz about bolts" repair videos. The throttle body has coolant that runs through it and often there will be a caramel like syrup in the intake brought in by the PCV system.

 

I had a same issue 2 yrs ago, misfire on 1or 2 and 3 techs including the dealer could not pinpoint the problem( we replaced ign coils, spark plugs, fuel injectors, cleaned the EGR body, nothing positive came out) my Prius was at 175k miles and one of my 2 tech that work on my car desided to open the coolant tank (mine is pressurized) and all the coolant went in system. For my tech that was a sign
of leaking head gasket and we stuck a camera in cyl2 , sure enough there was a leak from the head gasket that was squatting on top of the cylinder and coursing intermittently misfires . I end up buying a 35k ml. Used engine and replaced my original one. After all I opened the old engine head and looked at the gasket, I was shocked to see a flat sheet metal with silicone for head gasket , I definitely won’t be buying any 4cylinder Toyota’s from this point on . So far I put on 65k miles on my new engine with no problems at all.

 

EGR valve body is a bit tricky to remove , if you have not work on your Prius at all have a plenty of time look at YouTube videos on how to do it.

 

Videos by @NutzAboutBolts are all here:

Nutz About Bolts Prius Maintenance Videos | PriusChat

(Covering EGR and Intake Manifold cleaning. Maybe a little late now, but lots of good tips. The spark plug change video alone documents step-by-step how to remove the wipers and cowl.)

Engine swap by @Ragingfit with 4th gen engine here:

Swapping in a Gen 4 Prius' 2ZR Engine into the Prius v | PriusChat

(It's in the Prius v mods forum, since it technically is a mod, but basically an engine swap, and applicable to any third gen Prius as well.)

Here's a head gasket replacement video:

(These guys maybe have less than ideal "eating habits", but share a lot of good tips, definitely worth a watch.)