I burned some 15 year old diesel in my duramax truck. Here's what I did:
Filtered it out of the storage tank into my truck's slip tank through a 15 micron filter. Filtered it again coming from my slip tank into my truck's tank another 15 micron filter. My truck has a sump fitting on the main tank, so I am always taking fuel from the bottom - on my pickup, I have a FASS system that sucks the fuel through a water separator, and then pumps it under pressure (8 PSI) through another 10 micron filter - that's the fuel sent to the injector pump which has a Caterpillar 2 micron filter. Any fuel that does not get to the injector pump, is returned to the fuel tank by the fass relief valve. In effect, while my truck is idling, it is polishing the fuel. I had no issues with the 15 year old juice - and I know it was nasty coming out of the storage tank.
All that said: Your new Kubota with a common rail system loves clean diesel. Your tractor probably holds about 10 gallons give or take. I wouldnt risk the old fuel unless I had a good way to filter to heck out of it first.