I use to have a horrible and persistent case of plantar fasciitis and fairly frequent knee pain. I decided to wear those goofy ass things and in a few months I was healed. Since then I have made it a point to walk barefoot as much as possible and wear neutral lift, low cushioning shoes.
Thankfully I am married so I was able to bypass the inherent chastity feature of the Vibram Five Fingers.
I had similar symptoms as you and also tried the Five Fingers. I had similar healing experience. However I hated the feeling of these shoes with putting them on and taking them off. I realized what I liked was the lightweight footwear, neutral lift with a wider toe box, and a midfoot strike.
I found racing flats gave me everything I liked about Five Fingers, with nothing that I hated about Five Fingers, and they look like regular shoes.