Shifter shaft moving -- please help

We are putting on the pivot that goes from the shifter to the shifter shaft and we tapped it on with a hammer (lightly) because it wasn't lined up. When we tapped the shifter shaft slid back and the bike won't shift. When we pull it back forward it shifts properly. However, when I start the bike it sounds like metal is grinding. We took the clutch cover off, but am not sure what to do next.

Am I f#!#%@ ??

Please help!

If you need more details please ask and I'll do my best to explain.