I am genuinely confused - you're saying you have a pair of road shoes with no tread, but you ride with spd clips with them? That's the only way I can imagine that you could possibly use both mountain and road pedals on the same shoe.

What is the sole of the shoe made out of? I know a lot of people use carbon fiber soled shoes not because of the weight, but because it's so stiff the cleat doesn't cause a problem. Though...to be fair, for me personally the only shoes I have that don't give me hotspots on my feet are my specialized mountain bike shoes (entry level, but with a stiff sole not a "walkable" sole). For some reason my Specialized road shoes always cause some numbness. (Though my road shoes and Speedplay pedals cause me absolutely no knee pain, while my mountain shoes and pedals cause me a slight amount, so...haven't found anything perfect).

This isn't quite on topic, but I know Chris Balser is a professional bike fitter here in the cities who offers both cleat positioning and custom insoles. Would be pricey, though.