I don't know if this will help at all... but on the chance that your soreness is related to your plantar flexion, I'm having to do it in stages. My knees are pretty specific about what they want, and after years of riding with my seat height too high because of too-long cranks, I developed the habit of plantar flexing just to be able to reach my pedals at the bottom of the stroke. But over the years (and with contribution from mechanical issues in my other activities), that was giving me a lot of problems with my calves and Achilles tendons.
The catch-22 is that I can only lower my saddle by the amount that I've learned not to plantar flex, or my knees will give me trouble. The first cm was easy. After that, it took me over 8,000 miles to fix my pedaling style enough to drop it another 3 mm, which I did last week. So far, so good - knees aren't 100% sure about it, but nothing that's really alarming me, and calves are MUCH happier. :)
