I run and ride and it is very true - you do NOT use the same muscles. But, most importantly you do use the same heart and lungs. So if the endurance is there you are way ahead of the game. I always run with mild soreness and find it relieves it. If I am "very" sore, I don't run as it will always make it worse. If you're not sure, walk fast for 3 miles. Walking fast also uses different muscles than running, but it's as close as you can get. If you can't walk fast because of soreness, walk slow. Complete rest (like on the couch) is a huge mistake. Some people believe magnesium tablets help with muscle cramps, and many pro football teams drink the brine from pickles (tons of various salts in there) and swear it prevents cramping.

I find that cyclists tend not to stretch as much as runners. Did you stretch after your run? Never stretch before any exercise. Warm up is fine, but stretching should be reserved for afterwards. Overstretching can lead to soreness as well so no bouncing and no painful stretches. Good Luck!!!