I'm about a week away from hitting the 70k mile mark. Knowing that I would put a fair number of miles on the bike, I bought the extended warranty shortly before the original one expired. The bike has been trouble free with the exception of two recurring issues - headlight wiring harnesses and rear differential oil seals - all taken care of under warranty.
20,069 miles: right headlight wiring harness and differential oil seal
43,112 miles: differential oil seal
54,002 miles: right headlight wiring harness
61,971 miles: differential oil seal
67,538 miles: left headlight wiring harness
This time around, the tech (TJ at Romney Cycles) added an extra ground wire directly to the battery for the headlight harness. Based on experience thus far, it will take roughly 13-20k miles to see if this makes any difference. At Yamaha's insistence, the main wiring harness was replaced under warranty as well. Looking at the old main harness, neither of us could find any reason for doing this - there was no visible corrosion, overheating, etc. anywhere on the harness.
The oil seal issue is very puzzling - none of the three seals showed any nicks or damage, and each started to weep after approximately 20k miles. I do ride the bike offroad whenever I get the chance, and it is not unusual for it to be completely covered in mud by the end of the day. However, the third seal had a relatively "clean" life, which weakened our conviction that the seals were somehow being affected by dirt/grit getting in. In two instances differential oil was on the outer side of the differential, and the 3rd instance it was both on the innner and outer sides. I rode the bike approximately 1500 miles after noting the weeping the third time it happened, and the weep developed into a pea-sized droplet of differential oil which collected at the bottom of the differential.
I'm extremely impressed with the way the bike is holding up, and wouldn't trade it for anything else I've ridden. From an operating cost perspective it has been absolutely stellar, and from a reliability standpoint it has been awesome.
For anyone interested, I keep a maintenance spreadsheet for the bike and can send you a copy. Just pm me with your email address.
Chris