Even after fully rested (no diseases), when I am running, it sounds like I am almost limping. Then, when talking
to others, (first person view) I have to look up at them, and they look down to me. In Whiterun, for instance,
in the store, I can barely see over the counter.
In 3rd Person view, it appears that I am standing straight. Heck, even when talking to a little kid, he
is taller than I am!
Anyone have any ideas?

you used the setscale command on your character, maybe ?