Don't run barefoot, especially on anything hard like concrete, roads, sidewalks, etc. I saw someone back a while mention that. I know there was a huge craze to run barefoot a couple of years ago.. but it will kill you if you do it on a hard surface like the road. Best to keep to a field, grass, or one of those rubber tracks. You said your knees already didn't feel so good. & I wouldn't recommend treadmills either. I use them occasionally, but i've never had knee pain. My mom has knee pain & she says avoid treadmills. I'd trust her.
Keep up the good work. It will add a couple years to your life, hopefully in good health.