I'd echo what motorlaunch said as a first (cheaper) option. I noticed a difference in the feel of the ground under-foot when I changed my insoles. If it doesn't work, you still have some comfy insoles for other shoes/boots.
Can't help with the shoes recommendations I'm afraid. I have Meindl shoes which I find extremely comfy generally but I can feel rough stony ground through them, albeit not enough to bother me.