Not all the shift levers on the side of the tranny are the same. Some have the slot horizontal with the sides of the lever and some have the slot at an angle. Some are stamped offset to move them away from the side cover. I have found many problems can be resolved by swapping the levers from another transmission.

Does the rod look like it will interfere with the crossmember/body or is it just too short?

If the slot is not vertical can it be flipped over?

I would look for a different shift lever. If not then you may just want to cut the rod and weld in a piece of steel rod to lengthen it.