The shifter will shift even if it is "out of position" from its mounted position.
Why not make a plate and move the shift arm to where you want it to be?
Is the shift arm welded or bolted to the shifter? If bolted, this is easy. And if you want to move it to the left or right, just forge it with an off set.
I did this on mine. I had the same setup as you have. Had to move the shifter forward 3 inches and to the right about 1/4 inch.
Hope this helps.
