Some new shoes fitted to width and possibly some new insoles might be very helpful.
Also, I had the same problem with M540's and I switched to the touring version A520 pedal. It is only one sided, but it has a much wider platform that spreads the pedal pressure out. After that I didn't have hot spot issues (well, I did a bit on 80+ mi rides, but not like before).
Now I use road pedals, and there are some advantages to this set-up. But, you may want to try the A520 (or whatever it is called now) first. It is a pretty good solution for road bike/SPD set-ups.