The manual should give you instructions on the proper way to size a PTO shaft. You need to hook up with the PTO shaft tubes side-by-side and raise/lower the implement to where the distance between the implent input shaft and the tractor output shaft are the shortest. Mark it with a marker or something. Raise/lower the implement until the input and output are the furthest away from each other then measure the distance between the two marks you made previously. There should be at LEAST 6". If it's not 6", you've got a problem.
If you have 6", then remove and cut the shields first for both sides. THen use the shield peices as templates for how much to take off both ends of the PTO shaft.
Messing up the PTO shaft can be dangerous. Know what you're doing, or take it to the dealer to have it sized.