You are correct that the port stb fuel switches send that level sensor to the analogue gauge. Something has to convert a analogue signal, to the NMEA 2000 sentences necessary to be displayed on the Garmin chart plotter. The GFS-10 does that. You don't really need to deal with the digital read out in the Honda system--the wires from the tank will go directly to the fuel flow transducer, which does that function. Basically you are forgetting that there is anything "honda" involved--thus not connecting any honda NMEA signal to the Garmin...all is thru the Garmin transducer.
I would separate the fuel sensor output from the analogue fuel gauges and wire into the Garmin GSF directly on each side--ignore the switch--it will no longer be of use. The Stb fuel sensor is put in the fuel line,
after the filter, and has to be so the fuel flow is from top to bottom of the vertical sensor. Then you will have to access the top of each tank, and take that respective wiring, as per the diagram in the link above, I would use twisted, wire with foil covering (see what is there to the switch--that may not be necessary...but you
do want to have the ignition switch wired in--because you don't want power to the level indicated when you are not running the engine. You might be able to pick up the wire somewhere else than the top of the tank--but you will still have to access the tank top to be sure what the color code is (C Dory has often changed that--may not have in your boat--but check it).
I have not run the Garmin NMEA 2000 backbone, so I don't know if a separate 12 volt source is necessary for the "NMEA 2000 kit"--
http://static.garmincdn.com/pumac/2250_TechnicalReferenceforGarminNMEA2000Products.pdf This shows a separate power source--but since the GFS has a 12 volt connection for the fuel gauge, it may be redundant. Also be sure and buy the correct terminator resistors, so there are no open ports on the back bone.
Draw out the diagram, using the above manuals, and double check to see what parts you will need. I suspect that you will need one extra 10 meter cable, and probably another "T" than is provided. Not too expensive, and should work--forgetting about "Honda", because when you disconnect the tank gauge you will no longer get the Honda fuel readings....I would not risk having a NMEA 2000 plus the Honda digital on the same network, which may happen if you do not disconnect the wires going to the honda gauge...(I don't know it will cause a problem--just suspect)