Sounds more like weak or bad grounds or dirty switch, some times the wires are not soldered to the switch very well.
The system is pretty simple. Power goes to the flasher on the brown wire, then to the switch on the brown/white wire and then out on either the dark green of choclate wire to the right or left side lights.
If the flasher is anywhere near good then power will flow to the switch. If the switch is ok then power gets to the lights, with a good ground the lights light up.
Start at the brown wire at the flasher, does it get battery voltage? If so I might suggest making a jumper wire that can plug into the brown wire and the brown/white wire. This will send power to the switch, nothing will flash but things will light up. Once you get power to the lights and they light up well, then pull the jumper and install the flasher to see if the lights flashe.
Now continue traceing the wires from there to the switch, watching for where the power gets lost. If you have power clear to the lights then you need to check the grounds.
Stock both the front and rear get ground through the threaded part that screws into the body of the light. When bolted in place A ground wire runs from under the nut on the threaded part to the harness ground. Thats the black wire in the headlight bucket and under the seat where the rest of the rear lighting plugs in.
If at this point the lights probaly won't flash with the stock flasher. It's a load sensitive flasher. It needs two 27 watt bulbs and the 3 watt indicater light to flash.
Useing just the front or rear won't be enough load for the stock flasher. LED's won't either. Some small replacement lights use a 23 watt bulb, this won't flash either. You can get a non-load sensitive flasher at the parts stor. 522 or 533, can never recall just which might work.
I like the LF1-S-Flat from
www.superbrightleds.com It will flash just one LED bulb or up to 150 watts of lights. $8.95. The flasher come with leads that are in a plastic housing. Remove the wires from the housing. They have flat blade type ends on them. Just plug right into the stock flasher socket.
The flasher comes with either red and black wires or grey and black wires. Plug the black wire into where the brown/white wire is in the socket, the red or grey into where the brown wire is.
If you have a high output coil then you migt want to get the flasher as far away from the coil as you can. The coil makes the flasher act weird.I mounted the flasher on the front of the battery box.
Leo