the bike still wont go in to second but first 3rd 4th 5th 6th work just fine i have a video of the sound here's the link

 

This is going to sound dumb, but is it possible to install the gear backwards?

 

No there is no way to get it backwards, but now maybe there is a washer that goes between the gears that's missing. But we don't know how they put it together either. Second gear could have been shot before it was stripped down.

Here is a diagram of your trans, hope this helps you out. If any of those little parts were missing when you put it back together you may have to redo the trans, Or if second gear is shot.