The red connector is covered in another thread (safety switch?), will try and find it (quick search failed so far
)
As you are mixing & matching components from different machines (& the aftermarket) you will need wiring diagrams for each. At this point wire colour means nothing, just wire function. As wannabridin mentioned, start with the basic functions - ignition, start circuit, then work out to the others. On my build I put all the components where they were going to be, then started connecting things together. Mine was completely custom (nothing were is was originally
), so I had diagrams for (but not limited too) - the reg/rec / HID / changed starter system (relay) / Hondaman ignition / and 550 diagrams (different years).
Having a multimeter to test circuits will speed things up. Electrical is not hard, just takes patience, to sort through one wire/connector at a time.