Sometimes the truth lies between the extremes, and sometimes it has nothing to do with extremes at all. I congratulate you for moving from one kind of intense activity (slow-twitch non-aerobic) to an entirely different kind (fast-twitch aerobic endurance). What many who have gone before you (including yours truly in my own move from gym-rat to marathoner) have learned, is while running is a great way to train for many other sports that involve endurance, few other sports can prepare you for running, except maybe running. There is no shortcut, really. Otherwise, we would see ""Couch 2 Marathon" programs popping up everywhere, lol.
You may have heard that endurance running is mostly about slow-twitch muscles anyway, so why don't the years of exercise translate into instant success? It's because though most of an endurance race relies on slow-twitch muscle fibers, these gradually tire during the race, forcing you to recruit fast-twitch muscle fibers toward the end of the race, when everything starts to feel very different. These kinds of muscle fibers are best developed by running as I will later describe. Of course, this depends on how hard you are pushing yourself, but look at your exercise resume.. You push yourself -- a lot! This will still be necessary, but as Heather suggests, your ambitions are outpacing your adaptations, and it's time to change tactics.
The reason I mentioned extremes is, that your strategy for rehabbing from or preparing for more running has involved more mileage and more activity, including stretching - an activity that pulls muscle fibers just like a contraction, just in a different direction. The other extreme mentioned was rest, which is helpful at night and maybe one or two days a week at your age, but has little value for solving tight muscle problems. In fact, there are many cases of athletes resting kinked muscles for years without any resolution in sight. Vcackerman's post makes the very good point that there are things you can do in your down time to speed the recovery of your muscles, without the extremes of using them more or just letting them sit there. Foam rolling is one popular way to increase circulation and lymphatic flow in exhausted, tight soft tissue to speed recovery, without loading it further (if not done to excess). I use other more specific manual techniques on myself.
Although you were very fit when you jumped on the running bandwagon, what is happening in your muscles right now, at a microscopic level, is a lot of re-absorption of damaged, unnecessary muscle, and re-growth of new cells that are adapted for endurance sport. If running was just about muscle strength, body builders would be our best runners. What you have to do is patiently allow this exchange of one kind of muscle for another. While your strategy to do this with consistent increase in mileage appears to make sense, it is the other kind of muscle you need to concentrate on developing - namely, fast-twitch.
When I started competing, I went from 5k to 8k to 10k, etc. Starting with the 10k and moving to the Half is not appropriate for the kind of muscle you have built, in my opinion. The necessary tissue just isn't there. While you are working on rehab - which I highly recommend, no matter how good some workouts feel (think about how you will feel after, as in that 10k) - I recommend plotting an entirely different strategy, aimed not at mileage, which will become increasingly possible automatically, but aimed instead at speed. Except in cases of overtraining of experienced runners, the irony is that running short, fast power intervals will prepare you better for the long stuff. Trust me, the mileage will become easier by itself, once you master this approach. Longer runs are more about getting your feet ready to handle the pounding than they are about strength. As one gym-owner pointed out to me, mileage causes muscle atrophy. Just look at the toothpick frames of world's best marathoners, versus the sprinters. There is a definite muscle-editing process going on.
Right now, if you are preparing for a Half Marathon (although if I were you, I would reconsider any August Half in a temperate zone), there is really no need to be putting in 22 mile weeks, no matter what anybody says. Don't copy elite athletes. They do what they do because they can, not because it makes them what they are. The rest of us call these freaks of nature great because of what they can do, but if we try to do the same things to become great, we become injured instead. Distance running is a chess game with your body. You don't just open up by sticking your queen out there. The patient strategy will win, and yours will be to train some endurance into your fast-twitch muscle fibers, so they are ready to share the load with what you already have. In the bargain, you will burn more fat throughout the day and increase your body's production of HGH, which is necessary for speedy muscle repair and development.
Once your muscles are running on all cylinders, the miles will open up to you. Then, instead of just losing the muscle you have built so patienty over the years, you will also be building a different kind. While we are on the subject of tearing things down and rebuilding them, it is important to know that dynamic stretching before a run is falling out of favor. In fact, some studies have demonstrated that it does not enhance performance at all, and may even slow you down, by replacing kinetic storage and release of energy with elasticity and increased effort, perceived and actual. Many point to pre-run stretching as a way to reduce injuries, but this belief has also been unfounded. Once again, many of the greats have gotten away with it, but that does not mean it actually helped them. They just survive a lot more foolishness than the rest of us can.
As Galloway has mentioned in his injury-free strategy to marathoning, the best way to warm up for a run is to jog slowly or walk for a few minutes. You just need to warm up the muscles for an increase in workload, not stress the tissue cold-turkey. After a run, your muscles are numbed by endorphins. Stretching - especially protracted ischemic stretches like yoga - during this time, can do damage you will not be able to feel until later, as you have also found. Replace this strategy with a few minutes of walking to keep the circulation going, and gentle, unassisted (unamplified by ropes or surfaces) movement of the tired muscles through their range of motion, under their own power only. Anything beyond will potentially produce more damage, until later when you can feel what you are actually asking those sore muscles to do.
Resist the other common advice to ice your muscles after a run, because rapid chilling of muscles has already been proven to cause small contortions of individual fibers, even though the ice again numbs your ability to feel this happening. Yes, the greats have done it, but they can do almost anything and it won't hurt them. If you want to some day be as strong a runner as they are, do not follow the example they set today. So, put blinders on at races, because you'll see all kinds of idiotic behavior that is not beneficial, even though it is survived. I know I'm making it sound like "you can't get there from here," but that's the way it will really seem for a while. Then, one day in the future, in the closing miles of a full marathon somewhere, it will dawn on you that you have been completely rebuilt, that you really are a different animal, you really are a runner.
Here is something from muscle nerds, written for muscle nerds, but it is useful for its description of 4 phases of muscle dysfunction, at least one of which you currently have. Note the mention of no benefits from rest in one of these phases (1, about hafway down the page)...http://www.webmanmed.com/triggerpt.html
Some of what you have been going through with the upper back (rhomboid muscles) and lower back, can be explained with the aid of the foregoing link. The hip flexors in particular (Psoas, etc., there are several) can pull the lumbar spine and top of the pelvis forward towards the front of the body and give your back muscles real fits trying to compensate. I posted a youtube video of a Psoas release technique earlier in another thread, plus a video link to a doctor demonstrated, evidence based, general release technique. If you are interested in these, I include them here...http://www.youtube.com/watch?v=U8PrRTIRJIY
http://massage-glasgow.blogspot.com/2010/01/treating-your-trigger-points.html
Finally, a good set of speed workouts by Matt Fitzgerald of Runner's World (courtesy of Active.com)...http://www.active.com/running/Articles/Run_with_more_muscle.htm?cmp=17-3-925
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