You might want to loosen your shoes for longer rides (at least during the ride if it's hot out). If that doesn't help, then try moving the cleat farther back towards the heel. That can help eliminate hot spots under the ball of the foot, but I'd think a lot of that would show up by 2hrs. Do you use SPDs (you said you had used them for spinning)? It could be the small contact area of that cleat gets to you after a while.

Different insoles are also a good idea, because Sidi insoles are practically nonexistent. I like the Specialized BG ones with high arch support, but there are a lot of options. A cycling specific one will probably fit better (still be thin enough).

Stiffness could be part of the problem, but for some people with various nerve compression things going on in the forefoot, stiffer shoes are more painful.