Could be muscle tightness or the way that you run. Do you stretch after you've been working out at the gym?
When I started reading your post my first thought was you're trying to do too much too soon. I wouldn't suggest running 3 miles straight away as a new runner, your body needs to get used to the impact as much as anything.
I've had pain that sounds very similar. I found strengthening my feet resolved the problem. Now twice a day (usually when I'm brushing my teeth) I stand on a smooth surface with the weight over the front of my feet and draw my toes back under to form a bridge with my foot. then release and repeat 20-30 times. In no time the problem was gone.
Finished in 4:31. Getting to the Expo was my biggest challenge. You'd think there'd be signs as you come out of the metro station. I didn't think the cobbles caused any issues really. The drinks stations were a pain, more because runners stopped and stood drinking at the tables ????.
There also seemed a lot of corner cutting. Keeping your eyes open for Kamakazi grannies crossing the course also kept me focused.
All in all a great first full marathon experience.