Suweet! Just read your thread after seeing your bass on BBG. I ran into many of the same problems you did and enjoyed seeing your solutions to them. The bridge setup with primary's going through the body was inspired. I ended up having to shave 1/2" off the width of my neck when I switched bridges on my sixer. I also left the neck too chunky in fear breaking into the trussrod pocket. I'm going to shave it down but I want to finish the one I'm working on now first. It's just a simple matter of having the skills, but not the experience. Things crop up now or are overlooked, that after a dozen builds will just be second nature. I'm in my second build now and still figuring it out, but having a blast. Keep up the good work.
Here are my two builds. Six String Neck Through Bass Build Aerodyne Clone Build