I'm in a similiar situation. I'm also about 40 lbs overweight and starting to run again. I haven't run a step in the last 4.5 years (since I picked up biking), so this should be interesting. I also have a foot problem for which I wear custom orthotics. Before I started riding, even the orhtotics didn't remove all the pain, so that's why I bought a road bike in the first place.

Now I want to do this s-l-o-w-l-y so that I can do it pain free this time (like back when I was younger). I am using a modified 'couch to 5k' program. While cardiovascularly, I can run significantly more than the program starts with...my CV conditioning isn't my problem. I am starting with the version for beginners and I just skipped the first month of walking only because I can comfortably do 25 minutes of walking with 5 minutes of running with no pain. I've been doing it for the past two weeks now and so far, I am 100% pain free. I've had to repeatedly tell myself to 'follow the plan" because I want to challenge myself and do more than I should every time. It's a constant struggle but if it means that when I'm done, I'm injury/pain free, it'll be worth it. So far, so good!

I did just read that thread that Becky referenced and I'm going to look for a copy of Chi Running at my library.