Does it have a tall body lift?

Glad you asked! The previous owner took a piece of square tubing and used that as a spacer!  Also, can anyone tell me what trans that is? I want to order some parts. My guess is the white shifter heavy duty seat, and the round shift handle boot.

Trying to understand why it needed clearancing for the shifter.

It's like that because that's where 5th gear goes. the left and right shots are the amount of play 3rd gear has.