The cleats may be in the wrong place and causing your foot issues. What pedals are you using? The contact area might be too small, so it puts a lot of pressure on your foot.

As for cadence, it's not something that I pay attention to. The whole 90rpm-for-max-efficiency thing has some useful basis, but I wonder what proportion of its fame is due to some pro doing it. It really doesn't take into account people's individual physiology or fitness. Many people have to work up to being able to spin (pedal at a high cadence) "properly".
Another possibility is that you were trying to spin in too hard a gear. That kills me for sure. If I don't feel it on the ride, I will certainly feel it the next day.

Provided your knees don't hurt at the end, you should be okay.