You might consider unscrewing the fuel gauge and inserting a suction tube to the bottom of the tank to suck out whatever is at the bottom of the tank. This would allow you to pull from the bottom of the tank below the level of the fuel pickup. I'm in the process of doing this proactively to check for water at the bottom of the tank. You might also consider researching
Fuel Right
: it dissolves the biofilm off of tank walls and clarifies fuel, but that residue may still need to be removed from the tank. The
Boat How To
diesel engine course covers this topic extensively; I'm taking this course now and it is well worth the money.