When you say the Racors are only half full, do you mean that they are half full of diesel
after you fill them completely when you change the filters? If that is the case then I am surprised that you haven't had problems with the engine
The recommended practice is to use a 30 micron filter in the Racor which is installed before the lift
pump and a finer filter I think 5-10 micron before the injector pump
. If you have a second Racor what I would do is plumb that in parallel with the other with a couple of valves that will allow you to immediately switch from one Racor to the other. That way if one gets clogged at a very inopportune time you can quickly switch in the backup and keep going.
If you are seeing dirty Racor filter elements then you probably have crud in your tank and even better reason to set up the two Racors in parallel.