I have Shimano sport shoes, spd cleats. They are lace up, with no straps.

Yeah, I don't think it's the type of cleats that are causing the problem, or probably even cleat placement, though it's possible- I'm not feeling one SINGLE area of pressure on my foot, it's an ache along the entire bottom of my foot, and it starts as soon as I clip in.

Thanks for the isuggestions, I'll try switching inserts, etc.