Interfacing Arduino with Pololu JRK21v3 help please!

Just need to smooth out your analogRead() somehow.

void loop() // run over and over
{
  static int lastRawA2D;

  char Command[10]={0xAA,11,0x45,0xAF};
  int RawA2D;
  RawA2D=analogRead(AN0pin);
  while(1){  
    if (analogRead(AN0pin) > lastRawA2D) {
      RawA2D += 1;
    } else if (analogRead(AN0pin) < lastRawA2D) {
      RawA2D -= 1;
    }
    lastRawA2D = RawA2D;

    Command[2]=0xC0 + ((char)RawA2D & 0x1F); 
[...]