PTO would be unrelated, it is driven before the input to the Powershift part of the transmission. Likewise the range shifter is purely mechanical and is ahead of the Powershift input. If PTO or range shifter won't disengage then the conventional clutch (or possibly transmission internals) is the problem.
Powershift isn't hydrostatic. It has gears that stay engaged. These gears are shifted in and out of the sequence of power through the transmission by various hydraulic clutches that engage softly then are locked. Sounds like a clutch isn't disengaging. Most likely cause: dirty fluid plugged a control passage.
If the tractor is new to you - drain the transmission and clean the 'strainer' (hydraulic filter). What you find in the strainer can be a clue to neglected maintenance. If the fluid is milky (water) or dirty replace it. You might find the fluid flawless (not likely) in that case I would filter it and re-use it for now until you get the shifter problem identified. Pray that circulating clean fluid will flush the blockage out!
As for working on transmission internals - you will need a Service Manual, likely a pressure gauge, and access to gaskets and parts. That's way over my head (although I did bench overhaul a Hydramatic 50 years ago) so I would try the diagnostics in the Service Manual, then if that didn't fix it, take the whole tractor (and the Service Manual) to a specialist in Japanese automatic transmissions. He should have the intuition to know how to trace problems. I suspect the internals in these are about the same as a Honda etc A/T, less a torque converter at the input. A tractor mechanic familiar with Yanmar would be better but good luck finding one.
Don't be discouraged, these things are built to be repaired easily and inexpensively - if someone has the documentation and possibly a special tool or two.