Sparkylisle, I understand your question. What I don't understand is why bother? The FDC is set up to run perfectly fine to design specifications on #2 diesel as is with the FDC connected. If you bypass the FDC it will not be able to adjust the fuel delivery to compensate if for some reason you had to fuel up with something other than #2 diesel.
What if you were way out in the boondocks, running low on fuel, and can't find a diesel pump? You could still throw in some gasoline or kerosene to get you by until you can get to a diesel pump, the engine will still run fine, but without the FDC to compensate for the lower density fuel your power will be reduced.
Or, heaven forbid, you had to take a trip up north in the winter time to visit one of us damn Yankees and had to fill up with #1 diesel to keep your fuel from gelling up from the cold weather? Same problem, no FDC, no compensation for the lower density fuel, lower engine power!
About the only reason I can see for bypassing the FDC is if it is leaking and fuel is getting into the crankcase. BTW, if you DO bypass the FDC, it will increase the max fuel delivery rate. It is roughly the equivalent of cranking up the fuel delivery adjustment one full turn. Great for power, but really bad for the engine unless you install a pyrometer and get your right foot off the go pedal when the EGTs start to rise! When the military bypasses the FDC they turn down the fuel delivery adjustment to avoid melting the turbo, I'd suggest you do the same. AND install a pyrometer to keep yourself out of trouble!