If you had it in nuetral before the install, it probably shifter into a gear. Expessially if you had the detent balls out. If this is the case you need to find a way to get it back to nuetral, then shift it into a gear before you try to install it. The best way I have found is to lightly drop it(emphasis on light) on either the tailshaft or the bellhousing.
Yup you were right. I took out the tranny and dropped it on the tailshaft side (on a 2x4 so no damage) and it freed up that stuck gear. I made sure to put the detent ball back in and that it still shifted fine before actually reinstalling it all. So its a hybrid V6/Turbo trans now and shifts great. Thanks for the help.