Hello,
I also have a 2004 Hunter 36. We fouled our filters our first day coming to home dock. I can give a pretty fast/easy fix that has lasted for four years.
1) Unload fuel tank. (Pull sender unit out of tank and you can get a fuel transfer pump into the hole.) We were full so 35 gallons.
You could have that fuel polished, but we just donated it to the fire department. You get access by removing the bed, and the hatches in the floor of your rear birth.
2) Remove subfloor (It's a lot of screws, but doesn't take a ton of time.) Once completed you need to disconnect the tank and vent on the stern side, and the fuel hose to the engine. (Good time to replace fuel lines while doing this).
3) Take the tank out and clean it out. I used a hose to get the gunk out. I then coated the entire inside of the tank with anti-foul stuff.
4) Replace both fuel filters. (I toyed with putting a electric fuel pump here...didn't do it yet).
5) Getting the tank back in takes a bit of muscle. I found stern and vent + filler hose first, then muscle in the fuel line.
6) Once everything is reconnected you now have air in your lines. Bleed from the injectors.
7) We now only fuel up from busy truck stops/gas stations, never fuel docks. We also strain the fuel on the way in, then use fuel transfer pumps to fuel. I am consistently surprised how much gunk is in the bottom of the fuel cans. Diesel isn't the same as it used to be.
Feel free to reach out. Happy to help. (We ended up having to replace our starter also after this) It sounds like a lot but its a pretty easy job.
wp