This is exactly the clarification I needed. I read the GCX manual, and it seemed like putting the guitar signal through that device would in effect be double buffering (once through the guitar). What I suspect is that the GCX would attempt to "condition" the signal from the Waldo Buffer, and at the very least there would be some tone modification.
That's the trouble with being just inquisitive enough to be dangerous...mostly to myself
Thanks for clarifying the cabling stuff as well. I originally was thinking I'd build each cable by hand...but then I realized that between work, house, wife, grown up kids, & practice...it would take two years.