[blykins]

Take all the linkages loose from the transmission. Reset the shifter arms all to a neutral position. You can use an open end wrench to move the shifter arm shafts.

Once everything is in a good known neutral position, put the alignment pin back into the shifter and then reset the linkages to each arm.

I suspect that they are not adjusted correctly.

If that's not the case, then I would imagine there's an issue with the interlock pin that can interfere with forward/reverse shifter rail positions.