Do not think I had that issue. But I did start with a short shift adapter and removed it because it stuck up too high for a normal boot. I then added a 289 style shift handle. Do the side exhaust pipes exit centered in the openings? I did have a problem with the motor not straight in frame and too far forward because the previous owner(s) had the motor mounts reversed- side-to-side. That also offset the trans and it was about 2" too far back.
