I'd recommend seeing a podiatrist anyway[1].
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.
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.