Four thoughts for you:
1) I've often thought that I would install a tertiary (third) fuel filter IF I ever had problems...
Racor 30 micron > Racor 10 micron > to my CAT 3126's engine-mounted 2 micron.
2) I've often thought of installing one or two of these fuel polishing units:
Again... if I ever had problems.
3) But fortunately for us, we have never had problems with the fuel we have taken on. We completed our Great Loop, and have transited up and down the east coast without atypical fuel filter changes required. Maybe once a year?
4) I'm a big believer in these gauges, and I take a picture of the gauge at every weekly oil/engine check when underway. They have a "recording needle" so you don't have to be in the engine room to see what the gauge is reading while steaming along! https://www.racorstore.com/index.php.../view/id/12102
The forward end of the fuel tanks, on the bottom, is the "leveling" fuel line that lets the tank levels equalize. That would be a good line for a "polishing service guy" to tap, then they could send the return / cleaned fuel into the normal fill tank outside.
If you know your Mainship actually NEEDS the tanks cleaned out, that would surprise me.
In that case, there is more to your story that we would all like to hear about!!!