natejs

I recently bought a tranny off another member here. He ha the two pieces(bellhousing) unbolted so he could side it apart about and inch to show me the gears. Well today I bolted them back together and stuck the shifter in it to make sure it would go into gear.
It goes into first and second perectly fine but wont go into any others. Could this be caused because the two halves we re unbolted and spread apart a little?

If anyone knows why or could help that would be awesome!!

Thanks
Mike