One leaf spring eye to eye is about 1/4" longer than the other which may account for a very small portion of the issue.
Should I button it up and see if the new leaf springs, bushings, etc wear in and see if it goes back towards center?
A 1/4" over the length of a 5 foot torque tube adds up.
You could drill the centering hole larger in the
Spring Seat to give you a little adjustment room with the off set leaf spring bolt.
Other than that the rear motor mounts might be off a little.
I don't think you want the ball housing binding on the torque tube, it should line-up fairly close.
