2007 Surly Long Haul Trucker 54cm (Commuting/Wanna' go tour so bad), 1985 Trek 670 21" (Road), 2003 Gary Fisher Tassajara 17" (MTB), Cannondale DeltaV 600 (commuterized MTB), some junker bikes in my garage
A stiffer shoe should spread the pressure out a little more, and reduce hotspots. Of course a stiffer shoe is harder to walk normally in.
A stiffer shoe will be a big help, especially with SPDs. Consider Shimano's SH-RT50. I use the predecessor which is stiff while still being nearly as walkable as a sneaker. I have had no foot issues on distances up to 107 miles in a day.