As said, that engine is totally rebuildable. The reason dealers don't like to do rebuilds is that it's time consuming (extremely time consuming if they do it correctly). By time you figure in 20-30 hours labor at nearly $100/hr, plus parts, you're into replacement territory. Replacement comes with 1 year warranty, dealer rebuild usually 30-60-90 days. If replacement engine fails within one year, Kubota sucks up that $5000 engine. If rebuilt engine fails within dealer warranty period, the dealer has to eat it. Guess which way the dealer wants to go? Yes...replacement.
Do you by chance have insurance on it? They might help. Worth looking into for sure!
Also, if dealer replaces the engine, they are required by law to document the old engine's destruction. Meaning in order to get Kubota to send the new one, they have to take pictures of the drill bit drilled all the way through the block and into a cylinder wall. Thank you, EPA. Another reason to rebuild as opposed to replacing.
Yeah....loaning tractors is the #1 cause of tractor problems. I picke up a MF1145 last year for a song and fixed a few things. Dandy little tractor (still not a Kubota but I like it). I loaned it to my dad who was using it to spread some dirt with the FEL. My brother decided he needed to use it and he picked it up from my dad. Then my brother loaned it to his buddy. Needless to say I was not happy about it. I finally get it back and it's got more leaks than I can shake a stick at. I've been working on it ever since I got it back, fixing hoses, smashed hydraulic tubes, etc. Never again.