Flat foot problems

Hi, I have very flat feet and have had custom made orthotics for this which I have been using for several years, and I also wear them in my trainers when at the gym to avoid painful knees. They have been working fine as without them I quickly start to develop pain around both knees. However I have noticed since I've started running again I am experiencing a lot of pain to the inside of my shins. At first I thought if just pulled something and tried to carry on, but today I had to stop and it hurts to walk. Im presuming this is all related to my feet, and I was just wondering if anyone could offer any advice about where to go or who to see about this. I've tried to research shoes for overpronation but feel I need to speak to someone first. Any advice will be much appreciated!