It sounds like they are just "odd" soothing habits you have formed through the years. Since you are "gently" poking your thumb and only using folded paper and pencils, not really "sharp" objects (you can't "gently" poke yourself with a knife or pair of scissors, for example?) you probably did that back in your childhood accidentally and "liked" the sensation and the foot moment is common to lots of people, like hair twirling, or knee "jiggling", etc., its just comforting/soothing for some people. Otherwise I think it would fall under NSSI: http://www.scientificamerican.com/ar...-make-you-fee/. Some people rub their hands together ("Uriah Heep" in Dickens' David Copperfield had that habit) or do odd things with their hands compulsively/habitually, some people may pull on an earlobe or touch/tug on their nose -- there's lots of "normal" quirks people have.

Did you ask your psychiatrist about them? He would better know if you should see a neurologist, they're often compatible specialties one might need to see both members of. But I don't see anything "wrong" or different about what you are doing. You are aware since you have to fold the paper and probably makes sure there are pencils around that are "just right" to feel good. I use to take paper clips to therapy to fidget with when talking or rubber bands?