I also labelled everything. It's not completely necessary since the repair manual lists all of the connectors. My issue was more a matter of where exactly the wires ran in relation to the frame and other components. I came to the conclusion that is didn't matter too much as long as I can safely get each connector to where it is supposed to go without obstructing other components that will be mounted later (radiator, tanks, etc.). Hopefully, it will work out OK. There are two main runs, one down each side of the engine. The right side is for the rear break and ABS stuff, and the left is for the rear exhaust O2 sensor, rear cylinder spark plug, etc.
I am removing the SAS stuff, which will clear out some much-needed space inside. I probably should remove the charcoal cannister as well while I am in there.