Looks line I need some advice here!

I tried to start running again a month ago. I started with the C25K app and made it through week two before inner knee pain. This pain had plagued me for 5 years through both cycling and running. I've tried running three times in the last four years and am always dogged by my knees.

So I took 2 weeks off and bought some good shoes from the best retailer in town. They watched me walk all of ten steps before confirming that i have any inward gait that puts pressure on my inner knees. Makes sense. The new shoes feel great!

I ran this morning for the first time in 2 weeks and the knee pain returned, albeit not as bad. Wonderful, but ow. It's not debilitatating, but I walk at least 5 miles per day at work, so recovery is always slow.

I've come to the conclusion that my stretching is woefully insufficient, the muscles in my legs are weak, or something that needs to be diagnosed by a doctor.

My biggest problem is that I have no idea what I'm doing. I could use advice on good stretching, whether or not strength training is necessary, and if I'm in good company (feels like I'm the only 31 year old male that can't work out two weeks without injury).

And before the inevitable "see a doctor" reply, keep in mind that I'm researching the good ones in town that take my insurance. There are also a couple beginner's running classes in town, but both programs started over a month ago and I can't afford a trainer.