To be honest ive never set up *pedals* myself, so what follows is half knwing half guessing.
You said your pedals show ingame? Highlight them and "Set all Inputs" like you did for JS. Try if that works. If not, try assigning manually.
Again, highlight you peds in the middle. Then, on the left (AH Control) select rudder. On the right list (JS Input), highlight your respective pedal input. the SET INPUT. APPLY.
Check if it worked in "Settings"..... if you step on your peds, the rudder line in the top blue box should now move.
Dont forget to calibrate!
Good luck
.
Schatzi