Running Queries

Yesterday was my first run in two and a half weeks. It felt good. Well, it felt good at the time. My muscles are complaining today.
As a point of interest, I’ve now run over 9 km with my Vibram FiveFingers. My feet ache along the sides after about 7 km, so I don’t think I’ll be raising the distance much until that is cured. But progress is coming.
I wonder if it is changing the size of my feet? If my foot muscles are getting stronger, will they get bigger? Will I need to get different sized shoes in the future?