If you think the gear mesh inside the trans is wrong, it should be VERY obvious before you put the second case half on.
If the mesh is correct, the only thing you should need is the proper diff and slipper settings.
After the diff setting tips above, make the slipper really loose and tighten it a little at a time til the front wheels barely lift off the ground while you hold the rear wheels to the ground and punch the throttle quickly.
If you get this right you will not strip any gears.