When I set up my AFC you actually have to set the TPS by pushing the pedal all the way to the floor to record 100% throttle. Have you had a friend push the pedal to be sure that it's not just your AVC-R settings?
We really can't tell you anything about your pedal without seeing it, just find one in a junkyard or pull yours out and try to fix it if you think it's bad.
Played with the cable for a while today and finally I have 100% throttle. When I tried adjusting it, it would just always stay at 88%. So I took some pliers and pulled the cable as hard as I could, put it all back together and voila, I had 100% throttle. Who knows why I had to do that, but it works now. Thanks for the responses.