I just replaced the turn signals with LED's on my wife's Yamaha Virago 250. It seemed straightforward, wire-for-wire. I also replaced the flasher to slow things down. BUT, when you turn them on, all 4 flash. They worked fine when just the rears were replaced, but when I finished the fronts, the problem started. Also the indicator light on the dash doesn't work. I did not wire up the marker light circuit.
I had a similar problem, but it ended up I just short circuited something in the process of disconnecting and leaving wires lying about while I tested the connection of others. I checked the fuses and replaced one and that worked, maybe that could be part of the problem?