The risk with removing a QH is the PTO shaft being too long and damaging the tractor’s PTO internals and housing/ bearing. In effect you have shorted the distance between the tractor and gear box on the implement by roughly 4 inches.
Do not connect the PTO shaft, but check your length at lots of points along the travel of the lift/lower range of the 3PH. If it needs to be shorten, there are guides on here of how to do so if you need that help.