Motorcycle Questions? Ask a Mechanic.
I've been working on them and building bikes around them for a bunch of years and I've never had one that had a problem that was caused by anything other than an oil cooler that was added on. And even that one was still in good shape internally and the customer support they provided me for the parts identification was great. They are great engines.
You've checked most of the major stuff. If you have questions about it I'd suggest pulling the cam cover (right side) and just taking a look for any type of debris resting down in the bottom of the sump. If it is clean then I'd say you've got a good engine that you won't need to worry about.
On their website they show the engine codes for engines beginning with 2012 model that were actually put together at the factory. I'm not sure about the number for engines older than that, because they don't have that information readily available, but if you need information I can probably email my representative and see if he can identify what you have. The engines that were sold as kits and assembled by someone other than the factory could be of a little more of an issue as you never know the skill level of the assembler.
I hope this helps. Please let me know if I can be of further assistance. Thanks, P.J.