Insoles may help, but perhaps the pain is a consequence of the longer ride: as we get tired, we frequently engage other muscles to do the work, and that can lead to "new" pains. The shoes you are using look very flexible, so maybe as you got tired you started moving slightly different (e.g., dropping your left heel a bit more) and that stressed the ball of your foot more than normal.

I used to get some pain in the ball of my feet with SPDs and mountain bike shoes, but I have switched since to stiffer Sidi shoes (with good arch support) and Look Keo pedals. No more foot pain.