Stretch, stretch, stretch... power yoga great for runners.
Also sounds like you have a shoe problem. I have super high arches. After going through a mutitude of running shoes I finally settled into Adidas. Great arch support and, depending on your footfall, they have a shoe for all of us. I use the cushioned line, as I don't pronate or supinate, plus I'm a mid/toe striker.
Go to a good runners store and take test drives in a few different kinds.
Lastly, don't over train. It'll take a while for your body to get used to an impact sport. Run/jog every other day... rest or do none impact on the off days.
Find a runners club in your area so you'll have a group to run with when the long run days get LONG.