If the cut is not square you have to adjust squareness first by moving one of the mounting brackets away from the stop by the amount that the cut is out of square, move the stop to the bracket and then perform the following procedure.
If the two rail mounting brackets are against the stops in the MFT sides and the cut is square then all you have to do is release the pressure on the cap head screws holding the rail to the bracket to only finger tight.
Release the front one, with the rail upright, first then lower the rail, release and retighten the back one, raise the rail carefully and tighten the front one.
The rail will now land on the pin and the cut is square. If the rail moves slightly due to wear from the pin move the rail backwards or forwards slightly so that the pin lands on a new section of rail groove.