Hi,
There are small footprint Centrifugal Separators available.
If you are really stuck for space Joe you could and should look at fitting a Coalescing Type Filter into the line between pump and tank such as
http://www.parker.com/EAD/displayCat...&sMode=Details
I am not personally familiar with the layout of the tanks on your boat and don't know if you have a Day tank as such or if each engine sucks out of it's own tank.
If you don't have a problem with microbiologic growth in your fuel now it may be prudent to add some biocide when you fill up. The " fuel bug" can grow just as well in cold northern climates as the tropics. this is shown by the fact that it used to affect the lube oil in some North Sea Oil Field Vessels that sailed out of Aberdeen.
If you can send me a rough drawing of your Fuel System I will try to draw you a simple way to add either a Seperator or a Filter system to your engine room.