Runner's Forum: Sneaker issues?

I've been running in Mizuno wave 4's (Stability) for my training for my first marathon, and I put over 400 miles on them prior to the race. For the marathon I picked up a pair of Saucony Grid Sinister's (Neutral). I figured that I would give up some support for lightness and speed. I ran about 20 miles in them before the race and they felt great. I injured my left ankle snowboarding over the winter and it always gave me problems and hurt over the course of my training, especially during stretching out. After my marathon with the Sinister's my left ankle was fine, but my right ankle hurt more then my left ever did, and my left ankle had no pain. Why??? I thought maybe I was not running symmetric due to the pain in my left, but there was no pain and I never compensated for the pain during my 2.5 months of training. I'm sure it is the shoes, but why did they make my good foot hurt and my bad foot feel good? Should I be running with a neutral shoe for the left and a stability shoe for the right? Boy that is going to look silly.