When you pull the PTO assembly, just the rear plate and the PTO shaft will come out. Remove the snap ring for the bearing, and remove the shaft and bearing from the plate. Now you can remove the seal and reverse the process.
The tricky part comes when you reinstall the assembly back into the tractor. Getting the shaft lined up with the pilot bushing while getting the PTO lever to engage the shifter at the same time lining up the alignment pins may take a minute or two. To make things easier, remove the bolt on the transmission shifter cover that also holds the locking plate for the PTO lever, and remove the fill plug from the top. Removing the plug will allow you to see what's going on inside the case. Removing the bolt from the shifter plate will allow you to swing the lever further forward to engage the shifter collar before the shaft comes in contact with the pilot bushing at the rear of the input shaft.
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