How do you fix this?

The adapter that mounts the shifter to the tranny needs to mount the shifter higher so the rods can go over the torsion bar cross member. I have a B/E body tranny in my 68 Barracuda and need to make a bracket that moved the shifter forward about 9" to get it to the A body location.

From your pictures the tranny looks like an A body unit with the wrong adapter and possibly the wrong shifter. Straight rods will work the Hurst Indy shifter I am using came with straight rods for 1-2 and 3-4.