I recently got some SPD pedals. Initially, my seat was too high (old pedals added about 3/4th of an inch to height), and at the end of the downstroke, pulled uncomfortably on my knees. After even moderate rides (~5k), it would be painful walking up stairs, for example.
Anyway, figured that part out, lowered my seat, no problems for several weeks. Weather gets better, start ramping up the distance I travel, and now I find that I get a (much) less painful version of the same thing after longer rides (>40k) with a headwind.
Is it normal to get some soreness in your knees, or is this a sign that the seat is still not at the right height? Is there an algorithmic way to adjust seat height?