hey man,
it's your battery, believe it or not. i just had the same problem this week. the thing is; if your battery has JUSTunder the recommended amount of voltage to crank your motor, it won't, but your lights will look fine. these batteries need to have AT LEAST 12 to turn the motor over.
most 12 V batteries carry around 13-14V. mine had 11.1 V and didn't turn it over and i heard the ticking. that's because your "starter relay" (the thing you identified under the seat directly behind the battery with fuses) isn't getting enough juice to make continuous contact, and therefore clicks. just like the starter in a car when the battery is low. in a car you hear the cellinoid that makes electrical contact and is located on the starter itself.
i even tried unhooking my headlights to conserve some power, but no go (i'm guessing that the battery only had about 10V available when the lights were plugged in). mine's an '02 and i just bought the bike in sept. (leftover that sat on a salesfloor for a LONG time. that's why i think my batt's gone bad)
i checked on warranty because someone said tat battteries have a 6 month. but all that shit is in the gray area according to yamaha and the dealer. they want to charge it first, and from the research i've done on that and the people i've spoken to, charging gel batteries is supposd to be pretty good. so i'm confident. i'm gonna' take it to the dealer to charge because they claim to have a special charger that charges these gel batts (high voltage, like 18-20)
Let me know how you make out.