if the nut came off, it's an easy fix for a dealer-and kubota pays for it. And-kubota pays them real well for it, enough that they can pick the machine up and deiiver it back to you and still come out ok. That's assuming you're not more than, say, 50 mi from said dealer.
It's accessible from underneath, rh side. If you have a belly mower on it, it has to come off. if it's a drive-over (aka "easy-over" ) deck, the deck needs to come off and the bracket that holds the deck will also have to come off. I hate those decks. From there its just a matter of using one hand to move the pedal back & forth while you follow the linkage. On the transmission end is where the nut usually comes off. 5/16-24 UNF, and use a lock nut on it. Probably not a bad idea to put a little loc-tite on the nut before screwing it onto the ball stud but be sure to tighten it up before the loctit cures otherwise it makes it that much more "fun". I say it's easy to do, but it's kind of in tight quarters back there like everything is on a BX tractor.
Might not be that nut but at least if you can get under it and watch the linkage (engine OFF!!), you'll find your issue most likely. I figure it's either the nut or the ball joint itself.