Willk, you could let your genny polish your fuel. More about that in a minute...
I store my boat diesel in a 1200lt tank with no bottom drain and I lift the fuel out using a vane type transfer pump. Even after the fuel sitting for a long time (years) the sediment comes out easily via the pump. Obviously I can't guarantee this in your case but you may not have as big a problem as you might imagine. I simply use a copper pipe as the dip pipe and gently place it until it touches the bottom of the tank. The copper pipe has a 'V' notched out of the bottom end to allow the fuel, or crud, into it. Once the fuel is flowing clean I leave it. Plainly this doesn't clean your fuel or scrub your tank but it saves you clogging umpteen filters unnecessarily.
Ok, the next step. Since your genny appears to be running fine the fuel must be at least reasonable so I suggest the following based on that. You can polish your fuel by simply running the engine and allowing the fuel which returns to the tank to pass back to the main storage tank rather than the day tank. The return may not be on the engine side of the engine filters so if not it will need to pass through a filter on its return path to the tank, then the returning fuel will be cleaned reasonably. If you wish, it wouldn't be difficult, nor give you much down time, to install an extra large filter to the engine fuel line for cleaning purposes. I would guess that running your genny under no load won't use an excessive amount of fuel and therefore be cost prohibitive. Also, you will have the advantage that while your genny is running during an emergency, it will be cleaning it's own fuel.
Just a thought for you.