Clutch linkage not lining up in neutral after shifting into 3rd

If there's no slop in the shifter linkages, the right bushings in the right holes etc, there can be slop in the trans shift levers with either the nuts being loose, or wear in the shift levers themselves being sloppy on the trans.
Check for play/slop anywhere, use washers/whatever, - then go back and re-align the shifter rods back to "H", and try again.
Good luck.