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It is important to realize that your whole body adapts to exercise. Not just those parts that you read about in magazines and that you therefore consider important and critical. While you may only worry your heart rate or your VO2 max, your joints and ligaments also adapt to a particular type of pounding or stretching; your muscles adapt to the stresses they endure. Your feet adapt to striking the pavement, your shoulders adjust to the reach in swimming. All these adaptations are essential for you to get better and to endure the stress of racing.
These adaptations are not always pain-free, and may at times require a fair bit of remodeling. That takes time to do. Real remodeling goes on all the time and is quite visible on x-rays of long bones. As stresses change, so does the alignment of the bone matrix and the calcium deposits. And when stresses disappear, as in zero gravity, so does the bone. Similar changes happen in ligaments, muscle, and connective tissue. These are real changes that take real time to happen, so be patient.
People are often eager to "correct" what they perceive as problems. More so when these "problems" are accompanied by some aches or pain. This tendency is not just limited to the athlete. Coaches and even casual observers will chime in and eagerly recommend fixes. They may do so without you asking. They will note that your foot moves this way or that, or that you swing your leg out a bit. They will tell you to get orthotics, special shoes, or use wedges and adjust your cleats. As soon as you show the slightest sign of discomfort, tons of advice will follow. It is best to ignore it, however well-intentioned it may be.
A certain amount of pain and aches is normal and to be expected when you first start training. It is very important to give yourself time to adapt and not to intervene early to "fix" problems. Nearly everyone has some alignment problem or another, but nearly all will do fine without fixes. The ones who are keen on fixing are often the ones who suffer persistent trouble.
If you are too eager to fix things, you will end up making them worse. That means for example that you should always buy neutral running shoes first. Do not buy "support" shoes unless you want to train your feet to remain weak. Even if you "overpronate" or "underpronate," or whatever else the observant shoe salesperson advises you, ignore it.
It is important to realize that the stresses won't go away if you correct something. You just end up forcing your body to adapt to a different pattern. You may think you fixed things and now your body can get back to the important business of running, but instead what you have done is forcing your feet to conform to a funny shoe with a weird bump. And now your body has to adapt to that and to running. It is no surprise that we ultimately end up with people throwing out their shoes and going back to barefoot running.
The take-home is simple: do not ever correct things you "think" need correcting. Do not subject yourself to the latest money-maker of all, video-analysis. Video analysis has limited applications, for example in sports where body position matters and your body sense is a bit impaired as happens when your first start swimming as an adult. In those cases, watching yourself swim can be helpful. The problem is however, that once gyms, health clubs and coaches pay for video equipment, they tend to want to use it for everything, including "correcting mistakes."
Only correct things that cause persistent pain for long periods of time -say over six months or more. Or problems that get worse quickly. Always attend to those that show objective signs (such as swelling or increasing deformations).
In all cases, only correct gradually and give your body time to adjust. Best is always to back off a bit and see if things won't get better by themselves. If not, try small adjustments. Or seek the advice of an experienced medical professional. Someone who is used to working with athletes.
If matters continue to deteriorate you may have to stop altogether, at least for a while. When starting up again do so very gradually and ramp up slowly. If the pain is very well localized and very consistent, you may need to intervene more quickly as this may be indicative of a real problem. More diffuse pain that jumps around from one day to the next is generally less problematic, and more likely to go away on its own -although it may take months to years.
When I first started running, I suffered bad headaches after a few miles. These went away within a few weeks. But not without friends recommending that I run on trails instead. I also always had knee pain in one or both of my knees. This came and went for several years, before it finally disappeared. These days, my knees rarely hurt. Similarly my foot strike was very "off" and I twisted my ankle quite a few times (a reason why I prefer the road, it is flat). I also wore out my shoes very unevenly. Both the ankle twisting and the uneven wear went away entirely on their own. Now there is just a slight hint of uneven wear left.
Remember the old remedy for all problems: more miles. No whining either.