Based on all the seemingly odd places that my massage therapist finds knots and hot spots after a strenuous few weeks or months of high mileage training, long road race efforts, etc., I agree with CDR. Yeah, the hamstrings and major calf muscles are tight. The quads may be knotted. Glutes start to feel like they're in a constant state of "TT butt." The real relief comes when you dig into the iliopsoas muscles and the piriformis in the upper region. Then the ITB and short and long groin muscles start pulling the knee out of whack. In the lower leg, the peroneals start to burn, and anterior tibialis is tight all the way down to the extensor tendons in the foot. Despite using good arch support in my shoes, I need to use a tennis ball under my arches regularly to avoid foot cramps. My massage therapist has even found some hot spots in the tibialis posterior, which must be related to the arch soreness issue. I think some of the stuff in the feet starts with fatigue of the hamstrings and compression at the bursa by the sit bones. The lateral calf stuff happens when the ITB and minor and medial glutes are fatigued and tight.

So long as I can keep the major muscles loose, then I don't usually have problems in the smaller muscles and tendons involved in the pedal stroke, except maybe the peroneals, but those on me have had some issues from back before I picked up cycling due to some asymmetry in my hips. When I feel sore after a ride, it's going to be noticeable in the large muscles. Walk up some stairs, and the quads scream. However, it is clear to me that once the larger muscles began to be fatigued and overworked and have trouble recovering, then the smaller, more obscure muscles take a beating. So, it must happen on a smaller scale too, such as on one long training ride.