So I took it to the dealer with a pile of misfire codes on it. They claim to have followed the TSB and reflashed the PCM to something more recent.
The car comes back seeming a lot less performant, and with less lower-range torque. The engine, over a day of driving, gradually wakes up. Nothing happens for maybe 50 miles.
But then...it starts happening again. CEL on, engine misfiring and losing power, Torque Pro firing error codes on three cylinders.
At this point, not sure what to do. Would flashing some custom tune maybe fix it, since it seems like a purely software problem?