I experienced a lot of discomfort when I first tried to run. You need to rebuild those muscles, but you will get there with patience and perseverence. As OB said, try shorter bursts of running and keep to a run/walk strategy until you are able to run for longer periods. I also find hills to be really good for getting the glutes back up to scratch. Speed walking up a decent incline will really give them a good workout! As for shoes, I am currently embroiled in a sordid love affair with my ASICS gel nimbus 25s. The cushioning feels oh so nice.