New holland TD80D runs rough/engine surges

I have a nice new holland td80d tractor that I inherited from my dad about 4 years ago. the tractor is about 15 years old, has a tier 2 engine in it, so
no DEF. Machine has never been really worked hard and has only 500 hours on it. Recently the engine started surging, losing power and sometimes quits
completely. It acts like its starving for fuel, so did all the easy stuff, changed fuel filters and cleaned out the screen on the lift pump. No change so i
drained the tank, cleaned it out and put fresh fuel in it. still no luck. finally replaced the lift pump, still no joy.
funny thing is it actually runs better cold, as it warms up it gets worse. I read thru the troubleshooting section of the shop manual, and it points to
trouble with various parts of the injection pump (it's a Bosch rotary) but i have a hard time believing that a machine with only 500 hours already has
issues inside the injection pump. Any thoughts on what I'm missing or what next steps should be? Anyone know a good tractor repair guy near Williamsburg,
Va. I'm a decent hobby mechanic, but tearing into an injection pump is beyond my skills. I hate the thought of taking it back to the dealer.

A couple things come to mind - Is the fill cap not venting making a vacuum in the tank? Or could it possibly be getting air in the system from a fuel line leak? They will sometimes let air in even if you can't see fuel leaking out. That would be exacerbated if there is a vacuum in the system.

Placing a clear piece of tubing in the inlet line to the pump can be a way to diagnose if air is entering the system. Obviously the connections need to be tight so air does not enter where the tube was added.

I've tried running it with the fuel cap completely off, still no luck. I found a few cracked lines coming out of the tank when i dropped it, so i did replace them.

Does your tractor still have the water separator filter behind the right side footstep? Every TD series tractor I've worked on had problems with that filter sooner or later. If I suspect an issue there I bypass it to see what difference that makes. In most cases I remove it entirely. They're nothing but trouble.

I was having very similar problems with an 8240 but with much higher hours. I went over all the fuel line connections snugging them up. The problem went away.

Why do you think the water separator is the problem? I had a problem on my NH TD95D last year. IO never get an indication of water in the fuel from the sensor. How ever I was able to get a lot of water out of the drain. I cut the separator open after replacing it and I expected to see some filter material in it. All I found was a sheet metal cone and a big spring! I think the cone thins out the fuel and water mix and the water drops into the lower chamber because it's less viscous than the fuel. That's my theory any way.