First welcome to the MMI Afourian Forum.
My preference is like this ~ tank ~ shut off valve ~ filter/water separator ~ fuel pump ~ polishing filter. This way the pump get clean water free fuel, this will keep the fuel pump happier and debris free.
Also while pondering future diagnosing and tuning I strongly suggest a "REMOTE START SWITCH" as it is very handy for all diagnostics.
Also keep in mind when working on the A-4 keep the water valve closed so water does not fill the exhaust and get into the engine
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Dave Neptune