can you feel every gear still?
my shift tower bolt came out, and it was in neutral, just wouldnt go into a gear. if you can put it in every gear and you still feel the guides (put it in first, if you cant go directly sideways into 5th its still in.) then you are in trouble. i hear that a blown diff will make the car clunk when you try to move it, not sure though. a blown clutch would usually grab to some extent, so you would be able to make it move. if you can take the shifter and move it in a circle, then the gear selector shaft bolt is laying in the bottom of your tranny.
