Anto, what's your shoes/cleats/pedals setup?
About 12-13 years ago, I was using Shimano SPD cleats with mountain bike shoes (this, on my first high-quality bike), and I started having serious hot-spots and pain on the balls of my feet, after about 80 kms (say, 3 - 4 hours on the road.)
I went to my LBS (in Pretoria, South Africa -- some distance from Ottawa, Canada, where I'd bought the bike!) and the guys there sold me a pair of Sidi shoes with rigid soles and ratchet-adjustable fastenings; plus Look pedals and Keo cleats. Never had a problem since. That setup was expensive, though - like, very expensive.
Preparing for my new Raven, in the past year or two, I thought I'd try another setup so that I could wear shoes I could use for walking off the bike. I put the Look/Keo/Sidi grupo aside for the moment, & started using good quality flat pedals (MTS Light Touring, Japanese made), with Soma metal-and-leather clips. Nice combination. Then, I thought I could use good quality light day-hiking hoes with these pedals. Well, I could for about 50 kms, but no more: the soles of the shoes were too flexible, and aggravated a growing condition I have in my feet, "Morton's neuroma", again in the balls of my feet. Any distance above 50-60 kms became just too uncomfortable. I went back to my Sidis, etc. -- no problem. The key factor, I think, is the rigid sole. Maybe I could have found a stiff-soled shoe that would mate with my MTS pedals & toe clips; or maybe not. Either way, I didn't want to spend another couple of hundred dollars trying to find out, esp when I knew that my Sidi-Look-Keo setup worked just fine.
So, I went back to the Sidis, and kept my MTS-&-toe clips for my city bike (short runs for shopping, etc.) When I'm riding on the Raven or my old Eclipse, I take along some cleat covers for short walks off the bike on tarmac, etc., and for touring, I take along a pair of light walking shoes or 'Crocs' sandals, depending on the weather, the terrain, etc.
I never had any foot problems at all until I was in my mid-50's (a decade-plus ago now!). For the cycling, I've found that the combination of a rigid sole and a roomy toe box has worked for me. Oddly enough, I've never had any problems with hiking, cross-country skiing, etc.
Hope this info is useful, though I don't assume that my problems/solutions will work for others. My experience may suggest some things to discuss with your foot doctor, however.
Good luck in any case -- John
