and have been slowing trying to understand things.
When you understand a Glide Shift transmission, you can call yourself a mechanic, Grasshopper.
You can see from the schematic that when you shift 'gears' you are merely moving a selector valve. This starts to shift the gear fork, but before the gear moves another valve is actuated that disengages the clutch. Then the gear shifts and another valve allows the clutch to re-engage. The 4 -5 shift is more interesting because the 1-4 gearbox is shifting from 4 - 1 and the hi-low is shifting from low to high. The shuttle shift is similar but different. All this is finely controlled by small channels in the valve body. As a mechanical engineer, I find this system fascinating.
It is the reason I would always try to use the recommended Kubota fluid in a Glide Shift or hydrostatic transmission. You haven't harmed your transmission by mixing the 2 fluids, and I don't think it's causing your problem, but people have reported harsh shifting when using non-Kubota fluid. Engine oil is different - use whatever brand synthetic or not as long as it meets the recommended viscosity and API grade.
detour
I've stayed out (mostly) from the lubricant discussions. People use the word 'quality' a lot, and it can have 2 different meanings. The first is 'goodness', as in poor, better, best. The second is 'characterics', as in viscosity, clarity, density, etc. For example, Havoline may be a higher quality (gooder) product than Kubota, but it may not have the optimum quality (properties) that your machine needs.
I was riding with my sister in her older Honda Pilot one day on a level street when it gave a noticeable thunk. She said it just randomly did that and she ignored it. I found that it was a common problem caused by the automatic clutches, and that transmission fluid additives with friction modifiers are sold to correct it.
/detour
Your test results indicate that your issue is hydraulic clutch related. BTW, how well does your power steering work? It shares some parts of the same system?
If you want to do some diagnostics, you can check some pressures, but I think you'll need some special tools. You can see on the diagram that there are test ports for the main pressure, pilot pressure, and clutch apply pressure. The WSM has procedures and acceptable pressure values. Be careful and assume the tractor may move any time it's running.
But I would crawl under it, passenger's side just in front of the rear tire, engine off and trace the hydraulic suction line starting at the sump, through the filter and on to the pump including the side branch containing the steering/transmission pump and cooler. Any seepage is a point that air can get in. Remember that this is under vacuum and fluid won't squirt out.