I second your 'check out the drive' idea. Shafts aren't the sort of part you expect to break unless what they drive is seized. Sometimes a part might be inadequately forged and then break in service, but that's not common. If the pump rotates freely, alignment or spacing might be suspected.
I have a rule for myself. If I have to remove something to figure it out, I replace it with a new part unless the part is very expensive or the tear down is dead simple. I don't know about Kubota pump drives, but it sounds like an easy tear down. On my Ford, the pump drive is a shaft and gear that is driven off the crankshaft gear. Replacing the pump drive would take some work, because the timing gear cover has to be removed. In addition, the pump on my Ford is not serviceable. If it was me, I'd put in a new pump on general principal. Buying new parts every now and then saves the expense and aggravation (especially the aggravation) of having equipment where everything seems to fall apart at once.
