I don't suffer from arthritis, that I know of. Cool, no pun intended. I wonder what it's like to run up there. I'd get a professional opinion from a sports medicine pro. You sound like you're fit and capable.
Stiffness can be normal, and come from a lot of things.
A 12-mile run is still a long one. Maybe you are not used to the distance. Most veteran runners will tell you the body will talk to you certain days. I've heard that crosstraining is vital to running the marathon. Weight lifting is very important in order to make the muscles more capable of supporting the body.