If you manage to get a dead battery after a few tries of starting the bike, I expect the battery to be the culprit. I had this, not too long ago, that I could get a few tries out of a fully charged battery but it never really started. With my new battery I can easily try starting on the electric ignition for half an hour (not continuously, but still) without killing the battery. Check your battery voltage first.
Your clutch problem, have you checked your clutch cable? Is it not just a matter of adjusting that?
Flasher problems: check your wiring and your bulbs. I'm no expert, but if your relay is physically doing something I wouldn't suspect that to be the issue here. And as you said, it worked in this setup before, so there must be a bulb broken or a wire disconnected or something, your lights should pull enough current to make the relay work.