I would make one suggestion..
There is a shoe on the market by Vibram called the 5 finger... I understand there is allot of hype out there so I can only speak from my personal experience.
I have been doing 6 miles a day for several months I started running again in earnest last Oct... Well I have had a couple ACL and MCL injuries over the years...
That being said when I started back seemed like I always had some pain one way or another nothing terrible just a always knew it was there.. like you knees etc from time to time... some days good some days bad... At any rate fast fwd till I read this book called Born To Run.. it goes on to talk about running barefoot and the reason behind it.. well I wasn't going to do that but these shoes did enable me to run naturally again...
It was odd as I felt how I had to learn to run all over again.. so I put them on and went to it.. one minor note is I did not read the part about introducing them slowly into your routine...
Next few days I could barely walk.. lol... due to muscle fatigue... but that got better in the next few days as I built up the proper running muscles...
So now I am for the most part 100% pain free from any running activities ... I get muscle sore but never knee or joint pain period..
I don't know if this will work for everyone all I can say for 100% sure is it worked for me...
The shoes cost about $100 or so and it was WELL WORTH every penny to me...just thought I would share as I have been in the same spot you are... no matte what keep up the good work...
Kevin