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There is a second fuel filter, have you changed that? It's towards the dash on the right side (from the seat) or is on my 2017 3025E. What you are showing is a water strainer or at least that's what I think it is called on my version of the 3E series.

I would also take a look down in the tank. JD in the past has put a small strainer where the fuel line leaves the tank. I don't know if they have done that on this tractor or not but is worth exploring. That might be getting clogged intermittently. You might also have algae or something growing in the tank.
 

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I haven't replaced the other fuel filter yet. It's a foot or so upstream of the inline pump on y 3032e, also on the right hand side.

The manual is referring to the parts in my picture as a fuel filter and sediment bowl.

There is probably only a gallon of diesel left in my tank, but I have a pile of brush that needs to be burned... I was hoping that a free flowing fuel coming out of the tank would be a good indication that the there is no blockage in the tank, but I guess the positive pressure created by the fuel pump could pull sediment/algae into the screen. I'll check that after work tomorrow.

Should I go ahead and replace all the fuel filters now?

Thanks for the advice.
I would so you know what you have, that main fuel filter up stream is really easy to change. They are supposed to be replaced a certain hourly intervals anyways.
 

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I was able to get the fuel filter loose with a bit of rubber belting in between the filter wrench and filter. I took a video of the sediment bowl filling with fuel. It barely filled the bowl itself in 14 seconds. The manual says 10-15 seconds to fill the whole filter. Am I reading this wrong or is my filter filling way to slow.

I also took a another picture of the fuel filter. I am pretty sure there is organic growth on it. I have only run two tanks of fuel through the tractor myself and am not sure if the previous owners treated the diesel or how long the diesel would sit in the tractor between uses.

So it looks like at the very least I should get an algaecide to take care of anything in the fuel tank and rest of the fuel system. I'll empty the tank and make sure the screen in there isn't plugged. Is there anything else I need to do for that.

I am thinking that's a little slow. I would go with your idea to drain the tank, probably need to remove it and give it a good cleaning. I would also blow out the fuel line from the tank to your filter to make sure it's clean and isn't rotting from the inside. Once you get that part of the fuel system clean I am thinking maybe run some fuel injection cleaner through it. You don't want any of those clogged up, that gets expensive real quick. Looks like you have found or real close to finding the source of your problem.
 
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