It's very important to prepare your knees, Achilles tendons, and butt for a long grind. I prepare by riding frequently for several weeks and use a stair master for the knees and heels. (most of my long tours have been between age 45, and 62) A workmate, who was a 'runner', rode with me down the Pacific Coast. He didn't do much riding preparation because he believed he was in great shape. We had to abort the ride south of San Fransisco because, like you, his ankles and knees were so badly swollen. On our next mutual tour, down the Alaskan Hwy, about 1500 miles, he prepared beforehand and not only thoroughly enjoyed the trip, had no physical problems.