Intermittent shaking on start.

In my experience, when people are concerned about a running engine without warning lights / error codes it's because they make a bigger deal of it than it is. And granted, It's very hard to communicate how severe shaking is until late stage failure and atkinson engines do naturally have minor rough running moments at times.

Has your MPG changed much?

When was last time you put cleaned the mass air flow sensor & throttle body?

Also inspect all the hoses, sometimes this can be a vacume leak...

 

It's important to use a quality Denso/NGK spark plug on Japanese cars. Also you might have a bad coil, changing all of them, or just the one that causing the issue. At your mileage, I probably would change all the plugs if you haven't changed them yet.

 

Well you can switch out 4 with 1 or 2, see if it jumps to another cylinder

 

If you're more than 2 quarts low on oil you can get misfire codes, but sounds like you take pretty good care of your car so it's probably not that.

 

I had a very similar experience. I also replaced my PCV valve too.
I used a different vendor for the injectors that I had used for injector rebuilds on some VT908 diesel engines in a boat I used to tend. They did a great job on those injectors so I trusted them to supply injectors for the Prius. The key thing is that when you look on Ebay for injector vendors make sure that INJECTORS is what they do. That should be just about ALL they do. If they are selling injectors and old cases of spam and computer parts and stuffed animals and ... Find a vendor that just does injectors. I used NEinjectors603.
Glad you resolved it!

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Even more complicated is the top sellers of legit parts will compete with fake sellers on pricing... There's also loads of random cheap sellers that are legit that I take a chance on and rarely have an issue. The more you study who you're buying from the better...

Main thing to know when getting started is if you want to save money remmber there's lots of other Toyota models that have identical parts as Prius for a lower price because its not a Prius part.

 

That's a very good point Prius Camper. I used to have an "Ever Nimble Echo" which was a great little tin can of a car, but it would probably be on the road today if it were not for a hit and run. That has the same engine and I suspect other parts too. Quite a few cars in the Toyota Line up have that 1NZ type engine.
A similar issue occurs with receiver hitches. I have been looking at getting a bike rack and the class2 or 3 Prius hitches are comparatively rare and much more expensive. But I read about a Reese adjustable for pickups that actually fits Prius gen 2 cars and is 2" class 3 with 500lb tongue weight. I won't put anything near that but having a 2" hitch for ~40% of the price of a 2" hitch for Gen2 Prius. ($150 as opposed to $375 or more). One of the few things keeping me from doing it is not wanting to carry a bunch more dead weight I only use once in a while.

It's like we are Cadillac as opposed to Chevy.

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BTW Bob, love the stretch 6 door look you have.
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Keep us updated re permanency of the solution