This is the schematic I just completed of what I'd like to do:
I'll put switches inline in each of three circuits going from board 4 (front power board) to board 1 (main body board) to interrupt the brake lights, all marker lights and the reverse lights. After that, it's just running a bunch of extra wires and switches to interrupt or include the lights after they leave board 1 and head to the back of the bus. I'm also doing some reconfiguring of the wiring as well.
In factory form, the "marker lights" are the front and rear triple lights at the top center of the vehicle and have their own circuit. The "clearance lights" are all of the rest of the illumination to include the parking lights and tail lights. I am splitting the lighting to "upper" and "lower" so the "wink" functionality I put in will affect the top lights all the way around except for the front.
All of the marker lights have been replaced with 3 mode lights except for the front and rear triples. These new marker can be illuminated dim (clearance), bright (blink) and colored (blue.) I also added a light on each side, midway down the bus, inline with the lower set of clearance lights that flash with the blinker.