What you may be doing without realizing it is putting your ankle against the chair rung... I do this even if I am at the computer and couldn't figure out what was causing my ankle to hurt... Discovered it one day here at the computer and watched myself at the sewing machine same ankle and same position...
As far as the thumb, of course your thumb will hurt if you did a marathon of hand quilting, trying to finish something, beleive me I know... I try not to hand quilt for more then 2.5 to 3 hours a day... Use the sewing machine and do other things in the morning and read at night...
Hope this helps, have been quilting since 1986...