Mine really couldn't have been placed in wrong. The whole shifter nob is still attached to the rod, and engraved into the nob is the gear diagram, 1,2,3,4,5 and R. Of course, 1 is at the top, 2 is below it, and so on. Had I gotten it twisted sideways or upside down, the nob will show those numbers upside down. So there's only 1 way it can go in, and unless the installer is illiterate, there's no way to get the shaft in upside down or sideways.
Only thing I can think of off hand is that we may or may not have had the car in a gear. When we put the bell housing back on and the shaft and everything else, was the car supposed to be in neutral or in a gear? I remember we had to put the car in a gear to rotate the wheels to rotate the driveshaft so we can get all the bolts off, but I'm sure we took it out of the gear after we were done rotating them. Once we were reinstalling everything and putting the 4 bolts back onto the driveshaft, we had to rotate the rear wheels once again, putting it back into gear and rotating it to put the bolts back on. What's the proper procedure? Put it in a gear or put it in neutral? I want to have one more go at this tomorrow night, but I want to see what you guys say to do.