Overtraining, injury, or part of the experience?

Question
I started training for a half marathon about 6 weeks ago. Before starting my training plan I was running 3 miles at a time 3 or 4 days of the week, along with doing some weights, stretching, and cross training on the elliptical. I started a 13 week training plan and increased mileage about 10% a week and got up to running distances of 6 miles at a time and 15 miles a week. My cardio endurance is suddenly much greater than my leg endurance. I noticed my legs getting very tired and heavy the weeks when I did my 5 and 6 mile runs (PDR for now). I went back down the next week to 5 miles. Anyway, each time I would start to run my legs would feel heavy and like they were taking awhile to get going, but then I'd feel fine, until finishing. Upon finishing, even a 3-miler my left leg felt heavy and sore and the pain was radiating from around my knees up through my thigh, kind of like the muscle was pulsing. After a stretch I would feel much better, however since the fourth week of increasing mileage stairs have been difficult. My left leg hurts on the left outter part of the thigh where it "connects" to my hip, and  my inner leg hurts around the knee. At first I thought it sounded like an IT band issue, which made sense because my leg has been so tight, but it's my inner knee that hurts, the outerpart is fine.
When I got fitted for my running shoes they told me that I walk on the outer part of my left foot, like they often see in a high school runner. I'm 25 now, but did run indoor/outdoor track in HS and haven't run much until starting again in September.
I attempted to run Monday and had to stop 5 minutes in, I was "waddling" and couldn't get my stride going, I realized I would either hurt my leg more by dragging it along or mess up the other one by over compensating. I felt extremely defeated, but rode the bike at the gym for 25 more minutes without pain.
Most of my pain only occurs when I step forward with all my weight on my left leg and bend my knee a bit (ie running, stairs, lunge position).
I've scoured the internet trying to find an explanation for inner knee/outer hip pain and can't find anything. I've taken 4 days off and haven't done anything except take a couple of walks and it is driving me crazy.
Part of the reason I thought this pain was "normal" at first is because I've had some joint issues since the age of 17. I saw a pediatric rheumatologist for almost 2 years, the medications (including viox, naproxen, and celebrex did not solve my problems, my doctor moved away, & I gave up and was distracted with college) Since then I've dealt with my flare ups with regular exercise, which has kept things bearable. I do not want to go back to trying meds when they do not give me complete relief. My new primary care physician did find some "markers" possibly for arthritis in my blood work, but feels that at this point regular exercise is a fine way of dealing because it has worked so well.

Do I need to give up running for an extended period of time until I feel 100%? Can I still do things like stationary biking and the elliptical? I'm just not sure how much is too much if I want to feel better again. I have a huge fear that if I stop I won't be able to start again. I really love running because I can (usually) and feel like that won't always be the case especially since my joint aches started at a young age.

Thanks in advance.

Answer
Hi Lauren
You have a lot of problems that have to be addressed and i can't possibly  answer all of them properly with the kind of clarity needed in email.I would need to ask you many questions to get the answers i need to properly advise you to the necessary action you need to take to get back to 100% and continue with your running.Would you be able to call me here in albuquerque NM any time from 6am to 8 pm MT to discuss your situation?You can get my contact info on my web site.I look forward to your response and talking with you about your situation.I will go into complete detail.

ALL the best

John