You sound like you are doing very well with your program of study, diet, running, and lifting. Here are my answers to your two questions:
1. Exercise and upper body muscle. I was doing great at lifting (for me) this winter, and like JoeZ found that I was making steady progress in strength. Unlike JoeZ, I did not find the strength training to be beneficial to my running. My only real exercise now is speed training, as I try to run fast (again, for me) in preparation for the fall marathon season.
2. Protein consumption after a run. Personally, I find I have no interest in protein immediately after a run. I'll put a beverage in the freezer prior to a run, then drink that with a couple of multigrain bagels after the run. The September issue of Runner's World ("This Just In", page 22) recommends that you increase your protein consumption for any runs over 3 hours, with some of this consumption prior to the run and some following it.
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