COACH!!! Long time man how you been? Wanna go ride San Felasco in the middle of summer again? :-) I think about you and your bud every time I go ride there.
Hey, can you be more specific of where on your foot you get the pain? Is it on the sole right on the arch, outside edge, toes, heel, etc... If is all over the foot and shooting up your leg, you may want to get back adjustments. Core will help your lower back but not your foot. Also, try riding with the shoes loose when you get the pain to see if it goes away.
When I get lower pain, I know is time to see a chiropractor. I had been doing 1/month adjustments. I've kind of stopped going for two main reasons. 1) I am doing more core 2) I gave up on my wobble-naught laser fit. Wobble had me sitting on the bike on an agressive position leaning forward to free up the leg muscles to pedal instead of part time dedicated to support my upper weight on the bike. I went with a 0 degree stem and got a riser bar. I still have a flat bar on my SS bike and when I ride it, I get lower back pain specially on climbs or when I go over the 4 hrs on the bike. When I get that lower back pain, I usually have to stop get off the bike and do a self adjustment. Even if is a simple bend over and touch the toes for a few second, it helps a lot. I also had the RETUL done and while the seat, height, reach over, distances are the same to the wobble, the stem and bar were totally different. So now I am using the wobble measurements but the RETUL recomendation to cleat, stem, and bar recommendations.
If you did the RETUL with Roy when he was at AJ's, he is back on the fitting scene at another shop in Oldsmart. He kept all the data from the fits he did. If you need a small tweak you may want to talk to him about it.