Everyone who rides a bicycle long enough injures their knees and feet at one point. The OP has been in pain for years and is finally thinking about a solution. The bad news, there isn't a surgical or drug solution to this problem that is inexpensive and will fix it for good. Here are my answers.

1. Clipless --- If you are using them, it time to go back to platforms. It's very possible the pedals are causing the problem and don't think it's going to be easy finding a solution. No one really knows whether a change to a certain position will make your pain better or worse. It's all guess work.

When I injured my feet, I spent thousands trying to find a solution. I got rid of the clipless pedals and several months later, the feet were able to recover.

2. Lower gears --- The days of going fast are over. It's part of the aging process and there is nothing wrong going slow. I have every symptom the OP described but they went away after 2 years and I'm pain free. I cut down my riding and now go slow. Your body can recover but it's going to take time. A lot of time.