I'd be pretty concerned about that chainstay rub. I've seen the walls of chain and seat stays worn through due to that kind of rub. Add a little mud and voila! Your tire is now a 29" abrasive wheel! Maybe you should look into some wider cross tires? Or narrower 29er tire? Or at least a 1.95 with a lower lug profile (or just trim down the ones you've got if you're short on cash).