Knee injury

Hi guys, 

sorry if this question or similar has been posted. 

I have a knee injury at the moment which started about six weeks ago in the right knee on the inside during a 14 mile run (after 8 miles) wearing a neutral trainer asics cumulus during the run. 

Prior to this I was wearing brooks adrenaline and saucony progrid (mild pronation trainer). This was after seeing a podiatrist for posterior shin splints and Achilles tendinitis on both legs. He told me to wear a trainer that was neutral or mild pronation due to my gait. Shortly after I picked up the knee injury, run close to 40 miles that week.

I then went to a physio who hadn't a clue and said it was runners knee and felt the knee and said the cartridge deep inside might have some wear and tear and massaged around the knee. He told me to rest for a week and build it back up which I have and now I have similar pains in both knees. it is difficult to pinpoint the exact location of the pain when it comes on, but usually does after a mile running and when I'm squatting and walking up and down stairs. 

After the physio I went to another podiatrist and the first thing he mentioned was orthotics as I supinate after watching me walk 5 meters, however the first podiatrist said I wouldn't need these as I had an sole insole which moulds to your foot type and that would be sufficient. I am just a bit apprehensive buying these as it was a groupon voucher I used to see him in the first place and I have spoke to a few other people and again the first thing he mentioned was orthotics as we all have special feet type. 

I haven't a clue where to go from here or what to do, any help/advice would be greatly appreciated.