Adding control number

If it's always on each fourth page, you can use a script to add an annotation or a form field to the PDF file with the control number. To convert this dynamic content into static PDF content, you would then have to flatten each page that you've added that information to.

A script like this would work:

var p = 0;
var c = 1;
var inch = 72;
while (p < this.numPages) {
  // create control number with leading zeros
  var ctrlNr = c + "";
  while (ctrlNr.length < 5) {
  ctrlNr = "0" + ctrlNr;
  }
  // determine location on the page
  var aRect = this.getPageBox({
  nPage: p
  });
  aRect[0] += .5 * inch; // from upper left hand corner of page.
  aRect[2] = aRect[0] + .5 * inch; // Make it .5 inch wide
  aRect[1] -= .5 * inch;
  aRect[3] = aRect[1] - 24; // and 24 points high
  var f = this.addField("Ctrl_" + ctrlNr, "text", p, aRect);
  f.value = ctrlNr;
  this.flattenPages(p);
  p += 4;
  c++;
}