This problem is not confined to SPF's.My CSX 4000 has the same issue.
In my case with an FE, it becomes more complicated in that if I raise the right side of the motor to center the pipes in the opening, I then have the drivers side almost touching the footbox and interfering with the linkage. Been struggling with that one for a while. I suspect that the footbox would need to move over to make things right. Now
there's a fun little project!
