I finally obtained a 6x6" piece of PTFE (teflon) with which I could correct the rudder cable routing. Espectially on the right side due to the oblique angle of the cable run, the rudder cable would rub on the both the fore and aft ends of the fuselage opening leading to concerns about frayed rudder cables. Not a good thing.
I cut a piece of the PTFE and determined where it would fit inside the fuselage. Filed a notch in it for the cable to ride in. Clamped in place and drilled. No more rubbing.
Then I noticed that the aft end of the hole was still rubbing. I didn't want a big ol' glob of PTFE showing, so I cut a piece that was the same height as the fairing, and riveted that in place. No more rubbing.
While the left side didn't have any real issues, things were close enough that I decided to go ahead and install the same two rubbing blocks on that side as well, as long as the fuselage bottom skin was still off.