hi nick - yes, this is an interesting thought, but I too feel myself erring on the 'half measures' side of things
I don't run myself, due to damaged knees (not due to an excess of prayer I hasten to add) but have recently started to ride a bike. My motives? - to get fit, to enjoy the fresh air, and, if I'm honest, there is also an element of wanting to keep in shape (visually) ... an element of vanity...
I have found, as a rather unfit person at present, that the process of climbing the numerous hills around my home to be profoundly painful, and did ask myself, "could I turn this pain to spiritual ends?" - well maybe, a bit...
However, the problem with this, for me, is twofold:
1. It was pride and pride alone that got me to the top of the hill - I did not want to appear/feel weak; I did not want to be seen pushing my bike etc...
2. The motives behind the whole cycling enterprise are, for me, ultimately self seeking - not in an overtly negative sense. Perhaps there is spiritual value in treating the body with 'respect' - not damaging it permanently with excessive eating, drinking etc - keeping clean and so on...
There seems to be, in the notion of 'penance', an idea of 'negating' or 'denying' the flesh, rather than prioritising it...