I had a bike fit a few weeks ago as I was uncomfortable on the bike. Prior to the fit on this bike, I had pain in my right foot, would generally sit on my right leg some causing sores on longer rides, and would 'hop' around in the saddle constantly, front to back, side to side.
After the fit, my saddle was replaced as it was no longer stable, lowered 1.5-in (unsure of fore/aft), my handlebars dropped .5 cm by adjusting the spacers, and 2 shims were put in my left shoe (as I had mentioned that my previous fit from about 5 years ago showed a dynamic leg length discrepancy). My left foot is about 1/4-in shorter than my right, but I had properly positioned my cleats over the average between the 1st and 5th metatarsals.
As a result, the pain in my right foot went away entirely, but I then ended up with pain in my right Achilles. At the time, I was riding about 100 mi per day and doing about 6000-ft - 10000-ft of elevation whereas most of my riding is about 40 mi per day with about 2000-ft of elevation. I wasn't hopping around the saddle like I was before, but after having been in this position now for a few weeks, I am starting to hop once more.
The fitter said that my feet should generally be flat when pedaling and after the fit, they are.
With all of that said, my Achilles pain has vanished (mostly). I think that is since I'm riding much less with much less elevation gain. But, I did start to feel it come back when doing a longer continuous ride but still under 40 mi. I commute back and forth to work and that ends up around 30 - 40 mi. If I do that with little to no break, then my Achilles starts to hurt.
Aside from stretching, is my saddle too low? Why does my left foot / Achilles not bother me?