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We have the same engine, mine being 1 year older then yours. (1997 Yanmar) and both were installed by PSC. My Racor 200R Spin-on Series Fuel Filter/Water Seperators for Diesel Engines Manual details the fuel transfer pump before the filter, not after it. Sorry Moderator, that's what is in print.
The fuel tank outlet(s) on my 1997 PSPH are positioned above the Racor Filter, hence may be the reason why I do not have the fuel transfer pump that is installed in your PS? Is your transfer pump located in the bilge area?