you didn't mention how you fill from your supply barrels/cans/whatever ...if you use an electric pump that has a filter on it (water block, say) you can "polish" the fuel (try googling "polish diesel fuel") ...simply run it through the pump filter one or more times. If you don't have such a pump set up, consider investing in one.
As for the gas you put into the diesel, back when, it wouldn't have been a problem THEN ...but, gas, especially w ethanol deteriorates badly over time, which may have contributed to your problem ...
if you pump out from your can/barrel/whatever, I would not let the "intake" pipe go all the way to the bottom of the container ...you might cut it off at an angle, to be sure ...then, when it sucks dry you can either dump out the sediment/water or leave the sediment and water in the bottom, depending on how much free play you've allowed for in the suction pipe.
Also, if you suspect water in the fuel container, there are paste solutions you can smear on a dipstick, which will reveal the presence of water (that settles at the bottom). Again, you can google the paste or check with your friendly gas station...they often check their storage tanks that way.
Too long a post, I know, but filtering fuel on its way INTO your tractor's fuel tank avoids a lot of problems.