The car began shifting badly, and then there was a loss of power and vibration on the lower gear. There was a small about of smoking, but as the car shut off, it was stuck in park and wouldn't go to neutral to push to side of road. About 15 minutes later, it was able to turn over again. It seemed like while in first gear, it wants to shut down. In higher gears it seem to run fine, so I think it's a clutch issue.
As you know, the Mazda RX-8 has a rotary engine, which means that there are no pistons. While these are great engines, they do require a bit more attention than a regular piston engine. It may be possible that you are experiencing a failure in the automatic transmission, so I would focus my attention on the ignition system, mainly the ignition coils as well as the spark plugs.
Because the rotary engines are a bit more involved, I would recommend enlisting the assistance of a certified mechanic, such as one from YourMechanic, to come by and have a look at your RX-8. They will have the experience and specialty tools needed to determine exactly why your vehicle is having a hard time shifting in lower gears.
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