Thanks for the suggestions folks, I feel a lot less lost at this point. This was the best picture of the cylinder damage I could get with my phone. I know it's not too clear in the picture, but it looks like just the plating itself. The material below it is scratched for sure, but there doesn't look to be any big gouges. I guess I'll find out for sure after I send it in but I'm going to wait on that until I find out what's going on in the bottom end. Gonna be out of town again for a bit, but next weekend's goal is to pull the bottom end out of the bike and start taking it apart.
Sorry Navin, I think the chances of it being an East Coast bike are pretty nil. The PO said this bike has always been in CA. From what I understand too, it wasn't street legal from the dealer. It was plated before 2004, but he said that if the plate expires the DMV will take it away. I haven't really looked into that but I don't see myself ever letting it lapse. Here's the bike itself.