Help! With side window alignment

[tpickstone]

Hello all,

I am putting my '69 coupe back together and am installing the side window glass. Everything seems to be going well but when I wind the window up to the top position it won't go all the way up, and is a little out of alignment (see pic).
When it gets up to the position shown in the photo the big gear just "clunks" off it's top tooth and that's as far as it will go. It also seems to go down more than it needs too making me think that there must be some way to adjust how the small gear and the big gear interact with each other, but I can't see how. It all looks to be fixed in onbe position. I have adjusted the 4 bolts that hold the winding mechanism in to be as far up as they will go but it's not enough.
Has anyone had this problem too? I am probably missing something obvious.... Any help greatly appreciated.
PS. I aslo need a drivers side GREEN TINT side window as the replacement I bought by mistake is CLEAR. I'll post that in the Parts seciton

Thanks all.