Hi Nick
The pto shaft is easy to get out. sounds like you have all the oil out the back end, if so just remove the 4 bolts give the housing a tap with a hammer to loosen it and draw the shaft out( you might have to drop the draw bar frame down to give clearance too). To re install engage pto lever twist shaft to line pto splines/ hyd pump gear and insert back in.
Before you do this though do you know if the gear box holds its level

The seal between the gearbox pto drive box and the rear axle can leak. Also the one in the top rear of the gearbox can too, you need the pto shaft out to drop the drive unit off the bottom to change that( draining gearbox too) and its easier to split the gearbox/ rear end with the shaft out to if needed

.
To test mine I drained the gear box Had the hyd oil in put the gearbox plug back and let it sit a while then pulled the gear box plug and got about 5 liters of oil out again where it ran through. my top seal was good just the bottom was bad to test the top I repaired the bottom filled the gear box and let it sit and waited to see if the level dropped again.
When you get the shaft out remove the pto gear It is held with snap ring and key in shaft( take ring off and tap/ pull the gear forward)
Then you will see the bearing in the casting held with an internal snap ring, ( that can be an a@@ to get out) Remove the bearing and shaft from the housing and the seal is in the housing . G man has a post on here from when he did his raised pto seal That will explain getting the old seal out better than I can with no pictures.
If the shaft has grooves round it where the seal sits then it will need a sleeve or some guys build them up with chemical metal and sand them back flush if you dont do something in a short time the seal will wear and leak again

. I usually go for the sleeve though Personally .
on the hydraulics I have never had problems other than leaking seals or a stuck lever, from what ive done it seems to be supers that have all the problems from standing and stuck valves. Maybe Brian or someone could answer that better for you.
Hope this helps you a bit
Regards Robert