Now my pains are gluteus and calf related, but I think they are mainly because I have been pushing myself pretty hard. Gotta slow down a bit and give myself more time to recover.
I've known about my alignment issues for years - mega tight hamstrings and weak gluteals so I got my first pair of (corrective) running shoes from a local, reputable, running shop[2] after a gait analysis. I couldn't run further than 3 miles before the pain in my knee became too much.
The shop then referred me to a podiatrist and switched my corrective shoes for a neutral pair, with insoles from the podiatrist. Since then I've had no problems and have run a half-marathon and 10k.
[1] Not that I'm an especially experienced runner but I've known about my alignment issues for years and, with running in particular, really notice the difference the right correction makes.