I'm guessing you have only removed the plate where the two shifters come through, correct? (I hope you didn't remove the transmission and/or tear more stuff apart.)
Stephen slid in ahead of me while I was typing, but I'll go ahead and post this since it took 20 minutes to type.

(no offense, Stephen.

)
If you look at the square "tower" where the main shifter mounts, you'll see a set screw with a jam nut sticking directly out of the front. Loosen the jam nut and the set screw first, if you haven't already.
Shine a light down into the hole where the shifter goes and you'll see 2 square shift rails with notches in the middle of them. These rails have 3 positions each -left, center, and right. Use a long screwdriver or skinny bar and move each one to the center position so the notches line up. This will be neutral. Insert the shifter into the "tower" lining the hole in the front of the pivot ball up with the set screw. (the ball on the end of the shifter will fit into the notches in the shift rails) Tighten the set screw until the tip protrudes SNUGLY into the pivot ball of the shifter. Wiggle the shifter slightly and adjust the set screw so the shifter moves freely, but isn't overly "sloppy". Hold the set screw in place and tighten the jam nut against the "tower". Verify operation of the shifter and readjust as necessary. Reinstall the shifter boot and all other parts that you have removed for access and you should be ready to ride again.