The main problem is the fuel filter system design. It would be time well spent to make sure your fuel filter is clean. There is a good forum topic called "Ask the Techs" where a thread describes how to quickly change the fuel filter, written by dmaxalliTech.
After that consider adding a secondary fuel filter. There are several secondary filter choices out there. You could check poster's signatures for solutions. This site also has a forum topic specifically on fuel filters.
And, if you arent already doing so, look into using fuel additives to keep the fuel system clean of water, bacteria, and rust.
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