injectors rarely fail on kubota mechanical engines. Electronic, different story (but you don't have that). If in doubt, send them out. Similar for the pump. I don't have a clue why people keep saying "it could be injectors"...because the old style kubota injectors just don't die, ever. Oh nevermind I do have a clue. Inexperience. In my 30 years, i can think of ONE injector that I replaced, it was because Kubota asked me to (to rule out an engine knock) and guess what? It didn't solve it. Broken crankshaft due to hydrolock, which ended up being an owner-induced problem that kubota paid for. Starting fluid #1 problem and #2 problem, took it to a "shop" across town who diagnosed it as having low compression on #2 cyl, then added oil to the cylinder to get the compression back up. Hydro-locked, cracked the crank, and it eventually broke after they got it running. One of many reasons I don't have a lot of trust in "diesel shops" that don't regularly work on kubotas.
you mentioned that you had clearance in the #2 cylinder's valves and not #1 and #3. They should all have the same amount of clearance, which is specified by Kubota (.007" if I remember right?). If you had a few tight ones, they can sometimes cause problems but my question is why were they tight? USUALLLY a few tight valves means one of two things: (1) someone adjusted them wrong or (2) the valve itself and/or the seat are wearing differently then the others, at which time I'm going to question WHY. That would be a rarity. On almost all kubota engines that Iv'e run the valves on, every single time they are either all the same clearance on the looser side of spec, even after thousands of hours. 2 valves that are looser could mean that they're bent. That would certainly lead to compression loss and misfire.