It is not the pushrod that is the problem. The problem is the fork. The regular bellhousing and straight fork will interfere with the floor pan.
I speculate that GM moved the ballstud so they could drop the end of the fork while keeping the window in the same place. That hotfix must have been cheaper than moving the window. In 1982, they moved the window and used a straight fork in the F body and later again in the Y body, but by that time, the manual tranmission was no longer available in the Malibu.
Fortunately, you can use these later designed bellhousings, as discussed on my bellhousing page.