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Picked up my car today.
-The largest issue, and the last issue identified after all of the below was fixed was the throttle seals in the supercharger elbow and valve, which are supposedly known to have a faulty design in the early models that wear out and leak. The elbow was shipped back to Sprintex and they replaced the parts and bearings in the valve area. Sprintex shipped my parts to the wrong state so there was a week delay.
-The gasket/seal around the supercharger to the intake manifold had leaks. They replaced it. This took over a week to get the part.
-There were a lot of vacuum leaks in hoses that were brittle and aging after 10 years and multiple track days which needed replacing.
-The MAF sensor I bought to try to fix the engine code from Autozone wasn't reading correctly so they put in a Denso branded one.
-There were a couple small leaks in the JDL exhaust headers that were welded back up.
-They replaced the 2 sensors before and after where the cat used to be that plug into the headers.
-I had them clean, service and replace all 8 fuel injectors/seals. This was another multiple week even in which they were sent the wrong tool to remove the injectors then the wrong seals as the injectors on the older BRZs were different than later ones so the place they got those tools/seals messed up. This was a few weeks of headache for everyone as well.

Sprintex originally said leaks in the valve/elbow is normal even when the shop sent them a video of all the smoke coming out of it at idle. Doesn't leak anymore with their new parts.

My shop called the tuner at one point and asked them about checking the tune. They said it's not their problem and not the tune. Makes sense since the engine/tune has been the same for 8 years, but they could have been nicer and more helpful.

Special thanks to the guys at Jon Bond that service superchargers like the Sprintex as they were very helpful to my shop in discovering the Sprintex elbow/valve/bearings issue and getting Sprintex to put the new parts into the elbow.

The car ran well on my drive home and it's weird how the car is much quieter with all the leaks from the exhaust and vacuum. Pulls harder than my recent memory remembered. Finally this bad dream is over and I have a car again after 3 months.

This crap makes me never want to buy another combustion engine car again. I think I'll keep the BRZ forever and when Lotus or another brand makes an electric sports car that's under $100k, then I'll pick one of those up. It's been tempting to put money down on an Emira, yes I know it's still ICE, but don't want to blow all my money on a monthly car payment when I have a house to pay off first.