So here's the deal, I got my first road bike in June and was immediately and hopelessly addicted to cycling. I was trying to take things slow to give myself time to break everything in (saddle, muscles, flexibility...) and was generally riding about 15-40 miles a week. In mid July I began to have slight knee pain and by the end of July my knee was screaming. I stopped riding and made an appointment with a local bike fitter and physical therapist. He tells me I have weak hips and a tight IT band and with daily use of the foam roller and exercise I should be able to be back on the bike in 10 days. So I RELIGIOUSLY roll around on this self-inflicted torture device multiple times everyday knowing that I will reap the benefit once I start riding again. The day finally comes and as soon as I start riding the knee pain immediately comes back. That was three weeks ago. I have used the foam roller every day and when I ride I keep a nice easy cadence and avoid hills or anything that causes too much force on the pedals...but I'm still in pain.
The only other thing I can think of is my shoes. I'm riding with tennis shoes and platform pedals with a cage that's too big for my feet. Generally when I ride my feet are sliding all over the place and I'm wondering if that's causing some misalignment. My bike fitter told me that my knees stayed pretty straight when I peddled but that he would need to add 3 mm of shims to my right shoe (when I get clipless) because its natural rotation was slightly off.

So I'm in the process of purchasing shoes and pedals and should have them installed within the next couple of weeks...but I know there's a chance it won't fix the knee pain. Do you think there's something I'm missing or do you think clipless should solve the problem?
Thanks