Henry, you said that you have put 2 micron filters in your filters. This is topic of much discussion in other forums. The pros of using a 2 micron filter is preserving the primary filter on the engine. The Cons are this filter will plug more quickly and will need to be changed more often. Not being an expert, I rely upon mechanics who do this for a living and like doctors they all have an opinion. My mechanic said that for the Yanmar engine, the 10 micron filter is perfectly adequate.
The other issue with the filters, besides particles, is water in the fuel. Check that bowl and empty water seen-it is heavier than the fuel.
Anyway, the principle here is that 90% of all problems with diesel engines are caused by dirty fuel. The prudent skipper will (1) buy fuel from suppliers that are relatively busy because they probably have "fresher" fuel than others, and (2) change those fuel filters on a regular basis. A vacuum gauge on the fuel line between the Racor filter and the engine will tell you when there is a change in the pressure needed to pull the fuel through the filter-higher the pressure, probably a plugging filter. My mechanic says, change all the fuel filters every year or every 100 hours whichever comes first.
On the Laurie Ann, we changed the filters at 150 hours, 250 hours and at 400 hours: when we started our 90 day, 1,600 mile river trip, at the mid-way point and when we came back home to Seattle.