I learned a lot on my first tour of approx 1500 miles. Setting the correct pedal length, proper seat adjustment,
using proper stiff cycling shoes, not wearing cotton underwear with padded cycling shorts, setting a pace that
I knew I could maintain all day, and using the gears rather than try to power up hills. I averaged 85 miles a day
through mostly remote country. A fellow that rode with me down the west coast had similar problems as yours.
He was a long distance runner so took my advice too lightly about conditioning his knees and heels prior to the trip.
We both did conditioning rides after work, but he did only half as many as me and would head home earlier. We both
had bike shop pros make sure we had our bikes set up correctly, especially pedal length and seat position, and wore
clipless cycling shoes. While I would set a personal comfortable pace I knew I could handle all day, he would race ahead
when encountering long grades (taking a run at it) which put additional strain and pressure on his knees and heels. We
averaged 75 miles a day and by the time we got to San Fransisco he was done...both his knees and heels were swollen badly.
I was fine. On our second long trip down the Alaskan Hwy he set a doable all day pace, didn't try to push it up the long grades,
and took turns drafting with me during strong headwinds. We averaged 75 miles a day then as well but we both enjoyed the
the tour without any injuries. I found that for me, taking a 15-20 minute rest every 1-1/2 hrs allowed me to go all day at my pace.