Cant pinpoint knee/ankle pain

Question
I've browsed the questions already on your profile for knee and ankle pain.  I wasn't able to find a situation exactly like mine so I'm going to ask.
I am 30 years old and I am an average runner - I typically run about 3 times a week between 4-12 miles per day.  I've done marathons and half marathons and have been getting faster in the past few years (qualified for Boston this year) About a month ago I decided to start training to run a fall marathon and use an 18 week program.  4 miles into my paced run my knee started hurting so badly that I had to stop running.  I didn't do anything to injure it - the pain just came from nowhere.  The pain is very indistinguishable in that it almost feels as if it's 80% in my knee and 20% in my ankle.  The location of the pain is my left knee and the pain seems to be in the center and the lower left of the knee.  It almost feels as if I need to crack it - like there is pressure built up that needs to be relieved.  (My knees and ankles crack when I walk down the stairs...it's been like this since I was a teenager)  I went to the Dr. about this pain last week.  They took XRays of my knee and the Dr. spent about 90 seconds with me (yea - this was the Cleveland Clinic - they're supposed to be world-class - not this guy).  He told me there wasn't anything wrong and that I just ramped up my mileage too quickly. I didn't receive any advice or diagnosis.  Just basically that I need to increase my mileage more slowly.  So it's been over a month now and I've been barely running because every time I try I get the same knee/ankle pain.  The pain occurs when I bring my leg up and out (extending it) to take a step.  I've also noticed that it is very easy for me to make the pain happen after running if I pull my leg back (doing a motion that you would do to take off a shoe or sandal - sliding my leg and ankle backwards).  This causes the pain to immediately happen.

I am so frustrated because I took a week off and just got back from trying to run - I only went 1.6 miles and the pain started.  I am not overweight and I have been running since I was in middle school.  This isn't a scenario of someone who never ran or who was obese and lost a lot of weight.  I've been a runner my whole life and all of the sudden this dumb pain is causing me to miss out on one of my favorite things. I want to know what is wrong with my knee and what I can do to get better ASAP.  
Can you PLEASE help?  I will answer any additional questions.
THANK YOU IN ADVANCE!!!!!

Answer
Hi Amie
That doesn't surprise me about your experience with the doctor at cleveland clinic.It appears to me based on your good description you have a tracking and alignment situation leading to maybe a small case of chondromalacia.First let me ask you if we could talk about this over the phone.It would be so much easier to cover this and give you a more detailed explanation.If not i will do my best,but it is not easy to put thoughts in email.My phone number is on my web site.I'm in albuquerque.You can call right now if you want or any time from 6am to 9pm.

All the best

John