The key sticks out slightly and I can't get the key to go in any further. It seems like it bottomed out and it's the original key but I can't see why it would stick out like that. Is it supposed to fit like that or is there something wrong?

 

Are you sure it is stock key? If you can't drive it in flush, I think it is not stock. I would just cut it off.

 

Take it back apart and see why its not going in all the way. Maybe a burr.

 

^^^X2 ^^^ a needle file clean up should do the trick. Or slightly file taper/chamfer the other end of the key to fit .