Saltare has Crap in fuel tank....How do I flush it

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I recently did some fiberglass work on the Saltare near the fuel cap, which necessitated removing the fuel cap housing and all hardware around it. Like a dumbass I neglected to put a rag in the fuel tank opening where the filler hose fits on( I kept the ski locker in place instead)....Needless to say I think some dust, etc. made its way into the tank and the boat runs like crap starving for fuel(intermittent misfire mid-upper rpm's). I replaced the filter element on Friday and ran the boat a bit Saturday, it ran much better initially, until the filter captured more sediment.
Whats the best way to get the tank clean again....Continue to replace the filter elements or drain tank and flush? And is there a pre-filter on the pickup in the tank?
Thanks in advance!