Well I don’t 100% understand your statement but will just comment anyway about the PTO operation on my similar L185 but take them with a grain of salt because Kubota did do different thinngs with the larger tractors of the same series.
For the clutch there are really two involved in the PTO system. There is an overrunning clutch (ratchet) in the rear internals of the tractor. That allows an implement like a mower to continus to turn and not drive the tractor drive wheels. In the older versions of PTO there was not a disconnect so when the drive clutch was pushed down when operating a mower the tractor was still being powered to the wheel by the mower. I am pretty sure your tractor has the overrunning clutch built into it. If you can turn the PTO shaft in both directions (with the tractor not running) that may need to be repaired or replaced.
The second clutch is the main drive clutch that is operated by the pedal. It is similar to a clutch in any automobile. But there are a couple of different types of these clutches on tractors (3 types if I recall correctly). The original type (which I have on my L185 and I think you have also) is just a single stage clutch (like a car or truck). Pushing the pedal down disengages the clutch and stops ALL drive past the clutch. The drive wheels and the PTO are both disengaged with the pedal down. Both are engaged with the pedal up if the shifters are in a gear. A two stage clutch is similar but The PTO is engaged first, then as the pedal is moved higher then the drive wheels are engaged. So, during operation with the tractor in gear and the PTO in gear, if you push the clutch pedal half down the drive wheels are no longer powered but the PTO is still powered. Pushing the clutch completely down then disengages the PTO also. The third type is called independent and is exactly what the name implies- PTO clutch is independent of the drive clutch.
As to the PTO gearing, there are three PTO gears on the tractor. First is 540 RPM out on the PTO shaft, Second is a higher speed (750?), and Third is another higher speed (1000 RPM). In the USA most implements are based on the 540 RPM PTO speed so should not be run at higher speeds. There is a mark on the tachometer that indicates what engine speed is required to achieve the PTO speed (will be near full throttle).
For all the gearing on the tractor they are NOT synchronized gears so you do not shift gears if the tractor is moving. You select the gear (speed) that you want and release the clutch pedal. If too slow or too fast then you stop, select a different gear and then go. There will be some grinding of gears unless you come to a complete stop and wait for the gears to stop all rotation. There may still be a slight grind to get the gears to mesh but not a lot of grinding.
So if you can easily shift your PTO lever into gear with the clutch pedal released and the engine running, you may just have a problem in that shift fork in the transmission. There is a cover over that area to take the shifter off the tractor and you can then see the gears and shifting mechanism. It takes some finesse to get that cover and shifter back onto the tractor but the repair manual may cover that.