I've had achilles pain on long rides for a while. I generally get it after about 50 or 60 miles if pedaling really fast and hard. I am pretty sure my seat height isn't the problem. A veteran rider has halfway convinced me it is b/c my feet need to be angled a bit inward. This makes sense for two reasons. Firstly the foot naturally angles but is forced flat in shoes. Secondly, I'm flat-footed so for me the inside of my foot is even lower than most people. The natural solution is a wedge. I cannot find wedges here so I need to make my own and try them. Any other flat-footed riders have this problem? Also, any suggestions on do it yourself wedges to put under the cleat? I was thinking perhaps a washer (I use SPD) but I do not know how much to raise the outside of the cleat.
I was also paying attention to my pedal stroke and I think I might be dipping my heel a little, particularly at high cadence. what kind of minor adjustment might help that? Moving my cleat back a little might help right?
I would try moving the cleats back as far as possible. This costs nothing and is easy to do.
That would be my suggestion as well. My Achilles area started getting sore on long rides back in the days of toe clips. Fortunately I realized that the soreness had started shortly after switching a some leather padded clips that positioned my feet a couple mm farther back on the pedals. Got some longer clips and rode a double century the next day with no more soreness - at least not in that spot.