When you do this exercise to strengthen and realign the foot and calf muscles, you will feel the most residual discomfort in the muscles that are relatively the weakest. In your case, it is the upper regions of the calf (This is common).
Persist with the exercises, resting a day or two between sessions exactly as you would following any strenuous workout. You will find that the discomfort will disappear after a few weeks.
When running a kilometre your feet will strike the ground up to 1,000 times. That is a lot of stress especially when running on hard pavement, running uphill and down dale. So, if you are struggling with discomfort after just a few easy sets of calf exercises, this is telling you something. You need to persist. Make these exercises a habit for the next year.
The problems with foot pronation that you describe do not develop overnight and may have been with you from early childhood. You are not going to correct overnight a process that has been a lifetime in the making. We are talking about years, rather than months.
Carefully analyse your daily habits to identify things that might be contributing to the problem. When sitting, do you splay one foot to the side? Do you stand with duck feet? Identify bad postural habits and work on replacing these with good ones.
If you have a "short leg" and who doesn't, the problem is most probably due to a tightness of one side of the hip. Try lying on the ground and pull one leg firmly to the chest, hold for several seconds, then repeat with the other hip. Repeat 3-4 times.
The other thing to do is to get a thorough deep tissue massage of both lower legs, including the feet and ankles. You are sure to have tender, knotted areas which will interfere with strength and endurance of the legs, including being the cause of progressive pronation as fatigue sets in. Get this done weekly for at least 4-6 sessions.
While I see no benefit for orthotics, a pair of heat moulded Formthotics Shock Stop will protect the lower legs and prevent excessive pronation while not inhibiting normal foot action during exercise.