What a pain in the ass mounting that front fender is! I'm really glad Jeff included the longer bolts. After fighting with it for half an hour using the bolts that came with the bike, I remembered the two bolts that were taped to the outside of the box.
The tire appears to be undamaged. I removed the seat to get all of the packing materials off and found a connector undone. I'll look into the throttle cable closer tomorrow. Thanks!