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AFA your one rear light being less bright, that is usually a sign of a poor ground on that light. You can test it by using a temp ground jumper. Open up the light and wrap about 2" of bared wire around the metal bulb socket and secure with a piece of tape. hold or fasten the other end of the wire to an unpainted fastener or spot on the frame, test the light. If it brightens, drill a hole in the reflector for a screw and attach a permanent ground wire to it and run it to another screw in the frame. Don't ground it to the body, the ground between the body and frame may be the source of the issue.
The 6v flasher has a red and a black wire. I'm assuming that red goes to the power and the black is to the blue and yellow wires??? Still contemplating on purchasing the resistors instead.
You can't connect the yellow to the black wire, or your pilot light will always be flashing.
I guess I fail to see the reasoning for using LEDs at all, given the 6v system? They aren't any brighter, won't use less power if you have to add a resistor. Running a separate ground wire all the way to the front, for all your lights, will accomplish a lot more.