If that car has a MAF, and the boot is split after the MAF, it will cause all kinds of engine problems. Why did they replace the throttle body if the TPS was bad? Why didn't they just replace the TPS? Is that a drive-by-wire engine?

I'd let them replace the rest of the stuff and see how it goes. Anything major will have been diagnosed already. The transmission harshness is caused by whatever is causing the check engine light, because the ECU will tell the transmission will go into a bare-bones limp home mode.

Fixed.