I just took mine apart on my yanmar, not very difficult and the Kubota looks very similar. My Yanmar had particles of crud from sitting. Any moisture or particles will make them stick as yours has. The rack that slides to operate the throttle has marks and the gears have paint that have to line up with the marks. The pistons also are peened and an alignment mark matched with the gear so they are not off by 180. Make sure the cylinders are in place to hold the gears aligned. After repairing I would replace your fuel to be sure no moisture and start with a clean fuel filter. I made a tool from fencing wire in a large u shape to install the gears.
Ok. Just replaced the injector pump. Now it will start, but it runs only at full rpm. Much more than I have ever ran it at. Also when it does this I can turn it off, take the key out and it still runs. I did bleed the injectors.
It sounds like the pin on the rack is not in the u that controlls the throttle through the governer on the tractor. Open the access plate and make sure it's in place. If not you will need to lift the pump slightly to align the pin.