I USED to have the same issues.
I thought it was heel spurs.
I broke my ankle and asked the DR about my heel pain, and he said to get some 3/4 inserts for the shoes.
Thin foam things with a thick arch support, I forget the brand, and after wearing them a few weeks, I did not have any more pain at all.
The calf stretching helped a little, but not much.
Its all in those arch tendons....I never would have believed it, I was sure there were bone spurs or something.
I now slip the inserts in once and a while to prevent the problem.