As for the PTO, yes it does use the same oil as the tranny , but the diesel cleanup doesn't present any special problem with the PTO.
On the larger issue, it depends what you find when you try to drain the tranny. Brown, caramel oil may actually be a good sign and nothing more than the end product of oil emulsifying with water from condensation. Here's what I do.
Get the tractor on a level surface. Open the level plug (on the side, front left of the tranny case, handily located behind the brake rod). Then open the fill plug. Add kerosene or diesel until you get something running out the level hole. If it takes little or none that's okay at this point, just make sure it's full. Close up and run the tractor around. If you can find some work to do with it so as to warm up the oil in the tranny all the better, but not critical.
Then leave it set for a few days.
Draining is next. Open the drain plug. If oil starts (or maybe a little water first) running immediately, take that as one good sign. It's not uncommon for there to be a thick, hard and dry layer of sludge at the bottom. If you get a little water and then oil right off the bat, you can assume there's not a lot of hard sludge. You need to stop and ponder if this is the case. Where and how much are you leaking? The common points are the seals around the input shaft (a plit at the front of the tranny to replace) or around the differential shafts. Replace as needed, drain and replace your transmission lube and let it do its job of suspending the particualtes, and chage out after some period of operation.
Plan B is for when you find a thick cake of dry sludge when you open the drain plug and nothing drains out. This si going to sound a little odd, but if that's what you find, dig up though the sludge until all of the water is out and you're getting oil. Then replace the drain plug, and refill with diesel until it is full at he level check hole. No need to run it anymore. Go back underneath, and drain again. Measure what you get out. The tranny holds 5 qts +/-. If you get significantly less than that, I'd suggest opeining up the tranny and cleaning out the sludge manually, and flushing with kero/diesel. Here again, though, before refilling, you'll need to identify the leaks and deal with them.
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