I also have a 2013 CT200h, and like another poster on this site, it had about 130,000 when the engine light went on and it started violently shuttering on start in the morning. I had it evaluated at an independent shop and they found the code to be a misfire in cylinder 1. When they pressurized that cylinder, the coolant bubbled up, indicating a head gasket leak (the air escaped through the head gasket into the coolant system.) The shuttering in the morning was because the coolant leaked into the cylinder and the first few ignitions failed because of that.
I got quotes from that shop ($4100) and from the Lexus dealership ($7000) for replacing the head gasket. Then I found a regional shop (greater SF Bay Area) that specializes in Prius head gasket replacement (found them on Craigslist). They've done 1500 of them and have posted 30 or so videos on YouTube showing exactly how they do them. I called, they quoted me $1350, they came to my house 3 days later with their van stocked with replacement parts. It took two of them 3.5 hours to do it on the spot, and it's been running beautifully every since (a week now.) One of the costs (and delays) of the gasket replacement is machining of the head if it needs it. They keep a machined one in the van (along with other replacement parts like radiators) and just trade it out if needed (charging a relatively small fee for doing it - I think they said $175 or something, but mine didn't need it). They didn't try to upsell me at all. When a small issue occurred (some carbon blocked a pollution control sensor), they came by the next morning and fixed it without additional charge with no questions asked.
They told me these engines 2ZR FXE tend to need new head gaskets at about 130,000 miles. One of their videos explains why. Apparently, most of the stress on a head gasket comes when the engine heats up. The aluminum block and head expand, while the steel bolts that hold them together do not, so the head gasket is compressed. The more on/off cycles of the engine, the more stress this causes. Since hybrid engines are designed to turn off during drives and stops, they tend to fail more often than a conventional non-hybrid engine.
Could you share the information for the shop you used? Im in San Jose and had the exact same thing happen this weekend to my 2011 CT!
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