On the transformer's output side there are four wires, Yellow, Orange, Red, Black.
If you want 25VAC out of the transformer (rectified to 35VDC (1.41 X 25V) at the PMDX power supply board), connect the Yellow wire and the Red wire to either J1 input on the PMDX power supply board. Connect the Orange and Black wires to the other J1 input on the PMDX power supply board.
If you want 50VAC out of the transformer (rectified to 70VDC (1.41 X 50V) at the PMDX power supply board), connect the Yellow wire to either J1 input on the PMDX power supply board. Connect the transformer's Orange and Red wires together with a wire nut. Connect the transformer's Black wire to the other J1 input on the PMDX power supply board.