Not familiar with this tractor, but everything is founded in basics. The water-in-fuel issue, I'd think, could be dealt with by wiring up the sensor wires to an appropriate external resistance load (resistor): I suspect that it's functioning more as an "open," so minimal resistance should work (complete removal/bypassing of sensor may not work because it might be because the engine management system might expect to see "some" resistance. Of course, one would need to be diligent to actually inspect for water in fuel on a regular basis: maybe install, if it doesn't already have one, if it does, maybe add another one(?), a separate water filter. If the engine management system is derating based on the water sensor then This derating issue should be taken care of.
"Engine pressure problems that make it hard to start at times" - that would be fuel pressure problems. Here too I figure it's an issue founded in the basics. Either the injection pump has an air leak (failing gaskets/seals) or the fuel delivery system leading up to the IP has an air leak problem. As air molecules are far smaller than fuel molecules you can have leaks that don't leak fuel, they leak (in) air. Starting with excess air in the fuel tends to show up as lots of white smoke out the exhaust. Look to pressurize your fuel lines (and filter head and its bits), see if they can hold pressure (not sure what is a proper pressure to test with, maybe 10 lbs). You could also do the same post-filter, directing at the IP. DO NOT mess with any lines post-IP, as these pumps operate under/with very high pressures. Not sure why tractor manufacturers (well, I can't say I know about ALL tractor manufacturers, but I have yet to see it) don't use a bit of clear fuel line leading up to IPs, which would allow you to see if there's air in the fuel lines (my cars are this way). If these tractors have separate fuel pumps then I'd also be checking those out (a properly operating one ought to be able to overcome most air leaks).
Lots of other codes popping up may be the result of a marginal electrical system (perhaps some chaffed wires- keep in mind that just because wire may be inside a wire loom that doesn't mean that it's protected- over time wire looms can actually chafe the wires that they're supposed to protect!), or perhaps a bad/flaky engine management computer. I'm more familiar with older automotive diesel engine management systems on VW TDIs (VE engines), and these also can have some "basket case" of error codes being produced by/from bad/flaky relays. A wiring diagram is going to be essential for tracking down where the problems are coming from. Sadly, that no one seems to have gotten any solution from JD themselves, whom I'd figure most certainly should have picked over the very things I'm saying here, doesn't bode well for finding a resolution; always, however, it's ONE person who discovers the source of the problem, and perhaps YOU can be that person!
