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Careful about your knees. One of the guys I work with had similar knee pain, rested for a week and changed his seatmast height, said "I feel fine" and three weeks later was recovering from arthroscopic surgery brought on when his knees swelled to a larger diameter than his thighs (and this guy is a racer like me and has big thighs).

Fundamentally what happened was in the week off, the scar tissue built up and reduced his pain sensitivity. He hadn't actually gotten any better.

What he did:
- got laid off the bike for six months after the surgery
- went to PT to regain mobility
- got his bike properly fit by a bike shop
- switched to a pair of speedplays with massive amounts of float. Eggbeaters are a good choice too, as said above.

I don't mean to scare you, but the threshold between "ok" and "laid up for six months" is narrow.

One other simple option you might consider is switching from clipless pedals to plain old flat ones. If you're anything like me, even the floatiest clipless pedals are too constraining. Anyways, good luck!