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You have to be careful about installing extra fuel filters for the exact reason noted by fredbrillo. If I remember correctly, with the larger Mercury engines, if the flow restriction exceeds .25 inches of mercury at max flow, you can experience fuel starvation. I recommend you call tech services for the particular make and model of your engine and let the experts tell you which, if any, external filters/water seperators can be used on your motor. Trust me, I deal with Mercury's folks on a weekly basis and they will be happy to give you the straight scoop. You can call them at 920-929-5040 and ask for tech support. And always make sure you have your engine serial number so they can look up the info for your motor. Or just email them via their website and save the long distance charges.
I know we have a lot of corporate knowledge here, but it never hurts to get it straight from the experts especially when it's free.
For you Honda, Yammie and Evinrude folks out there, I'm only a Merc guy but I'm sure the same info is available via their websites also.