How about a little more information. There are no hydraulic lines connected to the PTO shaft, but the hydraulic pump pulls fluid from this cavity. Did you drain the hydraulic fluid when you worked on the pto seal and now have air in the hydraulic lines? If so be sure that you replaced the hydraulic fluid with an approved UDT or Super UDT fluid as required and that you added the correct amount of new fluid. Did you replace the hydraulic filter (if it has one) and clean the hydraulic screen (if it has one). I would normally start the tractor and slowly move the loader or other hydraulic implement including 3 point slowly through the range of operation several times and that will normally clean out any air that got in them. If you collaspse all cylinders when you drain them, then there is little room for air in the first place.
