I don't get chafing, per se, just discomfort if I signficantly up my mileage. It goes away with riding more. Actual chafing may be a lubrication, a chamois or a saddle issue--or a combination. I also get the same bone discomfort you do. Again, I find it goes away with riding more...just with a few shorter rides between long ones!
Muscle soreness...I've never had the ankle problem--cycling is the one thing that doesn't make my left ankle snarl at me! Just last weekend I had the knee thing, though, after a 36 mile ride. Never had it before with ~25 mile rides, so I'm looking for input on that too! Warm showers and a few gentle ride (~15 miles) spent in a lower gear than normal helped with the stiffness and muscle pain. (You'll probably want to do shorter rides than that, though!)
I take food with me even on 15 mile rides. A Clif bar (may I recommend the mint chocolate ones? They taste like Girl Scout cookies!) or a package of the Shot Bloks. A 24oz bottle of diluted Gatorade, the same size bottle of water and a Camelbak (depending on distance and the weather) are my friends. I definitely need to eat after riding. It'll take some experimentation to figure out what works for you.