foot problems

I have been cycling for about 4 years for fitness and pleasure. I started using Speedplay Frog pedals about 3 years ago after deciding to try being "clipped in" and doing some reading on bike forums and reviews on different pedal systems. I like the Speedplay a lot and got them for both my road bike and my 29er. About 6-8 months ago I started to notice a thickening and a slight tenderness on the ball of my right foot. At first I didn't connect it to cycling as it didn't bother me while riding. I increased my mileage this summer as I was training for a century ride and some longer pleasure rides. I used to do about 60 miles a week in the spring, summer and fall and increased that to 80-100 miles a week this summer. The ball of my foot started to bother me at night and I realized it was probably from cycling. After doing some more research and talking to sales people at my LBS I decided to try the Look Keo Max pedal system thinking the large platform would distribute the load better and mitigate the foot problem. I now have problems on both the right and left feet-still on the ball of the foot. I use Sole orthotics as I have had heel spurs in the past and wear them in all my shoes. I saw my podiatrist and he suggested Spenco orthotics which have more padding. I tried them with no relief. The problem seems to be the the joint between the metatarsal and phalanx bones in the 2nd and 3rd toes. I don't seem to feel discomfort while riding with the Speedplays but do have some discomfort with the Looks while riding. Has anyone had a similar problem and have you resolved it? My podiatrist says I may have to go back to regular pedals and wear some hiking or running shoes. I don't want to do this.