cyccommute Thank you for the advice and picture! (That is a sick tandem bike, btw!) This is my first bike build, so I'm trying to switch to right/front brake and left/rear because I'd like to use my dominant hand for the front braking and modulation. I honestly don't know if this is a good idea, because I have another commuter bike that has right/rear and left/front -- but maybe I'll end up switching the brake cables on that bike too, or just get used to it? I haven't fully settled on the brakes for the new build yet, as the build is going very, very slowly, haha.
I'm planning to use cable-actuated hydraulic brakes, i.e., the mech-hydro hybrid. I want to learn more about bike maintenance, and even though I used to have an MTB with hydros, hydro brakes are intimidating to me. I figured that mech brakes will be easier to learn on and repair on the road if need be. You and others have recommended keeping the rear brake cable external, so that's what I'll do!

Arrowana I did manage to poke around and somehow threaded the housing through the down tube. Twice on both sides actually! I followed your suggestion (so, 2-1-4 and 1-2-5), especially since that is similar to what the Park Tool video recommends for installing shifter cables. I didn't like the look of how much the cables stuck out around the headset. So I decided to go with Crankycrank 's original suggestion of 1-1-4 and 2-2-5. Much neater looking. I wouldn't do this configuration for EVERY bike, but I hope that it will work here.

I've only just finished routing the housing, and I have yet to tune-up the shifting, not to mention installing the brake cables...

The whole reason I am even doing a custom build is because everything I need on this bike is XXS or XS sized. The drop bar width is 360mm, the crank arm is 160mm, and the frame is 44cm (XXS). You can imagine how small and cramped everything will be once I attach all my accessories later, haha! Once I finish the build, I will post pictures!!