Minor problem, just a rough idle
Just a suggestion, keep your fluids filled correctly in trans, engine, supercharger. When is the last time you checked the supercharger fluids?
But you said, symptoms are rough idle when its in gear, and sometimes a hard shift into higher gears. I would say the rough idle is simply a tune up job. Some ajustments to the throttle position, or check the vaccum hoses for leaks (it sould be at 15-20 Hg at idle). Disconnect the Mass Air Sensor to see if it runs better without the senor. If disconnecting a sensor makes the car run better, without the sensor... the sensor is defective.
And you can run a self diagnostics test on the car with a voltometer, and read the error codes which will pinpoint the point where the system is failing. Reffer to the Hayes Repair Guide 'Error Codes', in the Emmissions & Exhaust System Section. There are a set of plugs on the passenger side, all the way in the back...you use those plugs to run Self Diagnostics Tests.
Good Luck
-Mike N