SMOKE!
 

I just put the supercharger back on and I started it up. It fired up after a few minutes of cranking. But there is LOTS of smoke coming from the exhaust pipes. The car hasn't run for at least six months. Will the smoke go away, or is there another problem?

What was wrong with the car and what was done to it?

The s/c went out (bearings) and I repaired it, put it back on and started the car. It smoked like crazy. It hasn't run for 6 months or more.

That's probably why, its probably oil beeing burnt off. If it was sitting that long.

Yeah, when my turbo's went out in my old Shelby Lancer and in my Shelby Lebaron GTC-SX they smoked like an old whore. After the new turbo's were put on they smoked until all the oil that was sitting in the exhaust system was burnt out.
If you don't want it to smoke and you are looking at getting a new exhaust system the sooner you get one put on the sooner it will stop. Most of the oil is probably sitting in the catalytic convertor.
Also, take the oil filler cap off while the engine is running to make sure no smoke comes from there and to verify to yourself that it isn't the rings or pistons.

O ring?
 

You did replace the yellow O rings didn't you? Steam was my first thought.