Try a new flasher relay first as it is only a few bucks. If that doesn't fix things then check that all lights, front and rear, are working because one bad bulb will stop all signals from working properly.
If it worked fine before you pulled the front end apart then I'd check that no signal wires got pinched at the base of the fork ears. Also, your fork ears act as a ground path to your headlight bucket mounts.Any rubber between your fork ears and headlight will negate this ground(happened to me). There is a green wire attached to each of the two mounting nuts inside the bucket, check that these are connected to your harness.