Hi, I had the same problem when I came up against the Molex connectors on my bike and making a y-harness to run my tour pak lights and run wires to a trailer plug in. What I did was buy a Molex harness from Electrical Connections, I believe it was under $20.00, that had four wires coming off of it for plugging into a isolator for my trailer wiring. I soldered off these wires(the four wires going to the trailer) the necessary wires to run the tour pak wires (running, stop, left and right turn), I just had to run a ground from the harness to the tour pak lights to make up the five wires necessary to run the tour pak lights and buy the amp connector and the pins to connect up to the tour pak. So what I have is a harness that runs my tour pak and also runs my trailer lights that can all be unplugged when I want to take off the tour pak, or remove the trailer wiring in case of warranty work. It took alot of research because of the connectors and the electrical and service manuals came in handy, especially the wiring diagrams. Also, I had to take apart one of the connectors on the Electrical Connection harness(part #07673) and turned it 90 degrees because the plugs didn't coincide with the functions (a mistake at their factory) so had to take the plug apart and turn the housing so everything would match up, a jeweler's screwdriver came in handy. I don't think I could have made the molex plug with the pins unless one had the necessary crimpers, I had the amp crimpers for the tourpak amp end and that was hard enough, but that Molex setup would be a bit@%.
http://www.electricalconnection.com/wire-harnesses/hrns-trailer.htmI pasted the above link but it doesn't have a clear picture of the piece I ordered but what it will look like is the Molex male and female plugs to go between your harness under your seat with four wires coming of the harness for the stop, running, left and right turn lights. Find the ground in the Electrical Connection harness wiring (there will be two black wires, find the one that plugs into the ground of your harness on your bike) and solder and heat shrink a ground "pigtail" to go to the tour pak amp plug with the other four wires I mentioned above. Then you'll have five wires. When I get home I'll take a picture of the harness so you can get an idea of what I made but I'm sure you can picture it from my description. Hope it helps a little.