Auto Wait 3,000,000 ms needed

I'm not entirely sure I follow, are you saying that you are running a bunch of tests and at some point during the test a random pop-up could appear which you need to account for? What is the pop-up and how is it triggered?

Some options beyond relying on auto wait >> You can try using aqUtils.Delay and creating your own loop OR use HISUtils.StopWatch to create your own timer. See some samples below...

This example stays in the loop while a certain page element property exists OR until 45 minutes has been reached (edit times as needed):

  var loopTimeout = 0;
  while (Aliases.Page.FindChild("WndCaption", "Retrieving*", 3).Exists) 
  {
    Delay(1000); // delay for 1 second
    loopTimeout++;
    if (loopTimeout == 2700000)  // If the loop has been going for 45 minutes get out of it.
    {
      Log.Error("Process exceeded the allotted time to retrieve data.");
      break;
    }
  }

This example uses the StopWatch approach and is just setting a cap on the timer (45 min) where you can do other stuff in-between:

  // Time parameters
  stopWatch = HISUtils.StopWatch;
  limit = 2700000;// 45  minutes
  
  // Start time limit loop
  stopWatch.Start();

  if(stopWatch.Split() >= limit) {
    Log.Enabled == true;
    Log.Warning("The process has exceeded the " + (limit/1000)/60 + " minute time limit.");
    stopWatch.Stop();
    break;
  } 
  else {
    // do something else
  }    

Change the logic to best suite your needs if you need to do other things while your delay/timer is running.