Symptoms are suggestive of an air leak in the fuel system piping. Boat fuel piping when ''compression'' fittings are applied are very subject to ingress of air; solution: (if thats the problem) is to install/replace with flared fittings. Older fuel oil filter sets used neoprene/BUNA rubber seals, modern filter sets now use EPDM (ethylenepropylenediaminemonomer) which dont ''age'' as badly as neoprene/BUNA. Carefully inspect the seals on the Racors, etc. for aging seals.
A visual inspection of the tank internals will quickly show if the need for cleaning is waranted. Cleaning is best performed by mechanical scrubbing the internals, followed by a high pressure wash with detergent, etc. If you have a thick ''black'' coating on the surface walls of the tankage that would indicated polymerization of old fuel, if ''slimey'' would indicate a bacterial infection. Actual cleaning is usually the best remedy. However, for future attenuation of ''particles'' you can apply an onboard recirculation/polishing system consisting of a dip tube to the very bottom of the tank, a 20µM ''depth'' filter, followed by a 12v transfer pump (wired to the engine panel) and a delivery tube back to the tank. The 15-20uM filter set is run any time the engine is on and will keep the resident particles to a ''sub-micronic'' level (due to % (wt.) removal of such particles at each ''pass''. For a bombproof system consider to apply an independent 2-3 gallon gravity feed ''day'' tank between the Racors and the engine ... so that if you have any ''problems'' you can switch to the day tank run for about 3 hours and ''sort the problem later. If you want the schematic of my system, email me direct. (I''m very deeply involved in filtration engineering.)