It is normal in your first year or two of running to go through a number of physical adjustments we often call "injuries," but I think it helps to avoid labeling them at this point. As you know, once you give something a label, your options for dealing with it tend to narrow down. You seem very enthusiastic about the sport and may have jumped into it with both feet. Like any major venture in life, the downsides are not always apparent, or even credible until later in the game when you have already committed yourself. Rest assured many of us have been there before, and have developed our own strategies for dealing with the aches and pains of the competitive life.. but each body is unique, and another's successful healing strategy may not be your own.
The beginnings of your pain and muscle tightness probably start with what you called overpronation, and it looks like the "shoe people" got you into a pair of over-pronation-ready shoes. These are designed to restrict pronation by stiffening the mid-sole of the shoe, usually with plastic that cradles the arch and prevents it from twisting. In general, these shoes are less flexible than neutral footwear, and that's when other problems can start. Groups of muscles that have worked together a certain way have to adapt to this change, sometimes with negative results.
Some people have hips, legs and feet that combine mechanically to require a little finesse at the end of the footstrike in order to maximize propulsion and spread out the impact among the many bones and joints of the foot (which remain the same even when the shoe changes). The more exaggerated this motion is, the more likely it is to be called "over-pronation." That little bit of extra work by your muscles can add up over the weeks and months to produce muscle fatigue, which in turn can cause overuse of secondary muscles in the group that is responsible for this type of movement. On the other hand, when the shoe changes, some of this movement may be resisted by the footwear, causing a different kind of accumulated fatigue. In either case, tired footwork can result in actual damage beyond soreness.
Just like driving a new car, running in a new shoe often requires changes in how you use the vehicle for maximum advantage and safety. If your legs and feet are the type that over-pronate, teaching them to stop does not automatically come with the shoe. Chances are, some of your many calf muscles are doing more work with the current arrangement. This does not necessarily mean you must change back to your old shoes, although many find this to be the easiest thing to do. You may need to retrain your running form, or to take other steps that make over-pronation less necessary.The two often go together.
This approach differs from simply restricting excess movement with shoes and/or prescribed orthotic devices. You move the way you do because your brain coordinates this movement to match what it thinks is the least effort to get the job done. It bases these decisions on feedback from muscles, nerves, the balancing mechanism of the inner ear, some genetic coding, and what you see and think is happening and has happened before. Your job is to think ahead of all this and set up feedback that will deliver better results. You first need to assess the physical traits you came to the sport with, and what you can do to change them for maximum mechanical advantage. When people think it is as easy as simply changing shoes, they are often disappointed over time. Regardless, if you stick with any system long enough and do not overuse it, you can probably train into any way of getting by, once your body adapts. The question is whether you want to run long, far, and fast, or just run. I'm willing to bet you want to push yourself further, and will not tolerate mediocrity. This means more growing pains, more adaptations, and a greater sense of accomplishment. Good for you!
At this point there is no magic solution, because it is far too complicated than that. There are things you can detect by looking in a mirror or having someone knowledgeable observe the way you run. You may have already done this in order to get the shoe. What you may not have done is find out why you over-pronate. This is because pronation is a chicken-or-egg question. Do you pronate because your arch collapses, or does your arch flatten so you can pronate? Do either of these things happen because the bone, muscle, and ligament structure of your foot demands it, or is your foot simply not conditioned to be stable? Does your leg rotate outward to protect your ankle and foot, or does the footstrike reflect restricted rotation of the hip? Are all these things related to shortened flexors of the hip, or to problems with spinal mobility? Do your three layers of gluteal muscles properly support your pelvis so everything below can work properly?
There are almost as many types of feet out there as there are running shoes. Not all of them are equipped with the same mechanical advantages for running. The shape of the heel bone and other bone surfaces, relative lengths of the metatarsals, flexibility and inflexibility of the many joints, ligaments, and tendons vary considerably by individual and matter a lot to things like pronation. A strong and balanced leg requires a strong and balanced foot. Once that is taken care of, other things may fall into place, while others may need further attention. Hips, glutes, and core muscles are commonly unfit for running.
When people move from the couch to the 5k, it is sometimes important to determine how much damage that couch may have done, before relying on muscular systems that are already in dysfunction, and may get worse when called upon to work much harder. These things are best done in stages, and it can often help to train for your training. It may be fun to just go out and run with what you have, but you will hit the wall a lot sooner if you don't increase your general fitness first. Running multiplies the forces acting on your balance and posture. Your lifestyle, which includes the dress shoes you wear, how much time you spend in chairs, and with your foot stuck on a gas pedal, will greatly affect how you feel when you hit the pavement.
You mentioned stretches. The word stretch is too broad a term for a yes or no, on whether it can help, because there are probably more wrong ways to stretch than there are right ones. In general, moving a muscle through its range of motion when it is healthy and warmed up has a beneficial effect, if not held to resist contraction, not held too long to allow for free circulation, and not done at risk to the joint capsule in use. The brain is educated by a stretch within its range as long as the stretch is safe. The resulting physiological changes are good as long as they produce no further damage, but no light will come on when your muscles extend to a range that does not contribute to the movements you plan to make. A certain amount of kinetic energy needs to be stored and released for efficient running, which is impossible when a muscle is too elastic without expending excess energy on contraction.
Some research suggests, for example, that the best stretch for a rear calf muscle simply invoves dorsiflexing your foot without any assistance at all, either from ropes, a curb, or the floor. This is because a muscle resists stretching the least when the antagonistic muscle on the other side of the joint is stretching it. You are basically training the muscle to release, rather than to resist. This is more important than a mechanical stretch because less energy is wasted when muscles do not actively contract on both sides of the joint. It's more complicated than that, but the takeaway message is that toned muscles store and release energy like a spring. Energy is wasted and injuries increase, when muscles actively oppose one another, or when the muscles and joints are hyperflexible, beyond usable range. All of these things carry over into your running, and affect your risk of injury. The kind of stretches that contribute to running efficiency are aimed at reducing opposition more than restriction, and resemble more the kind of stretching you might do after getting out of bed in the morning. Frequent repetition of these gentle movements promotes better cooperation between your muscles, and better awareness of their health.
In your case, the tight calves are the result of accumulated damage from training. They are protecting you from further damage by restricting your movement. There may have been too much movement from miles of overpronation, but restriction of movement by the shoes could have been counterproductive. You can rest them, ice them to ease the pain (but not to numb them for further abuse), massage them to increase healing circulation, and gently move them through their range of motion when they are warmed up, to un-train the restriction and ready them for future use. You may be anxious to go out and risk further damage. If it's just a little stiffness and you continue to feel better afterwards, that's ok. If the legs keep telling you to stop, and you go, just ask yourself which will make your calf muscles faster in the long run, healing or scarring?
The more you ask of your body, the more important fundamentals are. The most important of these are balance and restraint. The experience gained from years of running, and the injuries I've had, taught me to address the fundamentals of stability first. I balanced my left and right with slight custom modifications to my shoes. I balance my terrain by chosing running surfaces that do not slant too much to the left or right, and balance my intensity and mileage with a mix of short and long, fast and slow. Injuries taught me restraint. I have learned when to push it and when to back off by listening to my body, always trying to think ahead to how I will feel on at least the next few runs, and even the next year, as a result of what I do today. Risking it all and going for broke is fun, until you pay the price. Being able to run injury free the rest of my life is far more gratifying.
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