This is one injury I have not had to struggle with or endure, but I  know a tight quad when I see one.

If you could see all  the trigger points in your thighs right now, they'd look like swiss  cheese. Of course 40 miles at 41 is no picnic with quads that tight.  It's time to relax them. The quads connect directly to the kneecap,  which cannot track properly when quad tension is not balanced. Tension  is rarely due to all muscle fibers pulling at once, but to small,  sensitive areas of micotrauma called trigger points which in turn cause  the rest of the muscle to protectively splint.

Even though you can't see the problem spots, you can  find them individually if you try. Scan the (relaxed) leg with your overlapping  thumbs using moderate pressure. Start at the middle of the quad between  the knee and hip bone. Then, move up to the area just toward the center  of the thigh from the hip socket. These are two places where Rectus  Femoris typically develops trigger points that manifest as knee cap pain.

Next,  move to the fleshy part of Vastus Medialis just above and to the inside  of the knee. Staying on that muscle, move about halfway up the thigh,  still to the inside of the Femur bone.

Lastly, the huge outer  quad muscle Vastus Lateralis is the trigger point capital of the world.  You can work up the center of this muscle sandwiched between the Femur  and the ITB that partially covers it. Finish near the knee itself, just  above on the outer mound of the quad, and slightly  under the outer aspect of the knee joint where ITBS is usually felt, by  reaching under the ITB itself while seated. These areas all contribute  to and translate into knee pain when tight.

Many people  are tempted to stretch tight muscles in order to lengthen them. If  muscles were made of taffy, this would make sense; why not just tone or  stretch this pliable mass to the desired length and tension? Muscles are  made of living, reactive tissue that is more likely to tighten the more  you challenge its apparent autonomy. There is another approach that is  more effective, and takes into account the special relationship between  the automatic portion of your brain and the muscles it directly controls  (the conscious mind only controls them indirectly).

To simplify this process, instead of trying to force  the muscles to lengthen or contract, open a dialog with the pain itself.  After finding sensitive spots in the muscle (trigger points), press  them with your fingers to intensify the pain. This simple act will draw  the brain's attention to the dysfunctional portions of your muscle, and  force the brain to recalibrate them. It's as simple as that, but you can  expect to have to repeat this process several times over weeks to  reverse long-standing neuromuscular patterns of behavior.

While  all athletes should master this form of damage control, more general  maintenance such as foam rolling can keep the muscles flushed out,  similar to a very basic sports massage. In your case, while it is  possible to relax those quads to normal function, an aggressive training  schedule and the aging process will both require this more proactive and  specific approach to muscle health.

Here's an interactive visualization tool:

http://www.getbodysmart.com/ap/muscularsystem/legmuscles/vastuslateralis/tutorial.html