okay, i'm going to go right through your list, and tell you what i can. if you have any questions, pm me. i wrote you a great answer and then i lost it, so i'll do my best to remember what i wrote.
stretches: what kind are you doing? when are you doing them? i will try to scan in my docs and send them to you-- pm me with your email address. (provided, of course, that i can still locate my books.) also understand that all the muscles in your lower back and legs affect each other-- in fact, all of your leg muscles either originate or insert around your knees, so a calf 'pain' could actually be a hamstring or quadricep issue, depending on where it's located.
ice: make yourself some ice massage cups:
1/2 of a cheap-o paper cup filled with water, freeze. then flip it over and peel the cup away from the ice, starting at the mouth of the cup. you'll be left with a ghetto ice popsicle, and a paper end to hold on to. apply that to your legs with PRESSURE-- it's not supposed to tickle. use circular motions, that move from your ankle toward your heart. this not only increases blood flow to the area, but in doing so, helps move by-products, such as lactic acid, away from the area, where they can then be reabsorbed by the body. healthy blood flow also promotes new tissue growth on the cellular level-- which means that any broken capillaries/ microscopic muscle tears, (these produce lactic acid), that you have, will heal faster. moving the blood toward the heart is also the reason why you elevate your feet. i also recommend that you get in a swimming pool-- you don't have to swim laps, but you do have to move around. the compression will actually make your whole body feel better, and it is a great way to recover after a hard workout.
because this is an ongoing issue with you-- not an acute injury-- you can subscribe to the ice/heat club. ice, then heat with moist heat, (a wet towel warmed in the microwave, but don't catch it on fire), and then ice again. this constriction and expansion of the blood vessels, again promoting healthy blood flow.
be careful with the ibuprofen. it is actually very addictive, and you won't even know that you've developed a dependency, until it isn't available/ isn't availble in the dose you've been taking.
do NOT run on the balls of your feet unless you are sprinting, or mimicking richard simmons. in fact, if you do that over a distance, you could easily hurt yourself. (and your fellow oc's, who didn't know that simmons was going to be in their ocs class.) the proper form for distance running is to strike with the heel first, and then follow through to the toe. i'm sure if you run in a park, you'll see people doing this. there's more of a cushion this way. running on the balls of your feet can actually cause you to get shin splints-- think about where the transfer of energy is going. (the time/amount of foot on the ground is much shorter/much less for the toe strike-- that's why it's for a sprint.)
calcium pills: unless you have a diagnosed calcium deficiency, don't waste your money. your body absorbs what it needs, and no more than what it needs, from the food that you eat. you'd be much better off drinking a glass of 1/2% or skim milk every day. what calcium that doesn't get absorbed by your body is flushed out as waste, so if you're already getting what you need, (milk, multi-vitamin, etc.), there's no need to take it. it cannot build your bone density.
(dude-- flymarines-- who is your oso?!?!???)
bone density: don't. do not even entertain. you bones grow in length until you are approximately 18 for women, and 24 for men. your osseous tissue will continue to grow in density until you are in your mid-30s. there is nothing that you can do to help it along. any rapid weight gain, be it bone, (if that was possible), muscle, fat.... unduly stresses your joints, and again, causes inuries to ligaments, tendons, muscles, and can actually cause you to break bones. (force/torque applied under a given set of conditions. don't get freaked out-- just understand how the physics works. lever, fulcrum? if you know those concepts, you're almost there.) unless you live in a lab, there is nothing that you can do to increase the amount of bone mass that you have, so don't buy in.
if you have any more questions, post them here for everyone's benefit, or pm me.