XY Plotter/CNC style interpolation project. Need great deal of help

There are some places where you have used == where you should have used =
Where you assign to a variable you need to use = not ==

Change this:

  if(digitalRead(xStopMin) == HIGH){
    xIs0 == true;  
    xPos = 0;
    Serial.println("xMin");
  }
  else xIs0 == false;

to this:

  if(digitalRead(xStopMin) == HIGH){
    xIs0 = true;  
    xPos = 0;
    Serial.println("xMin");
  }
  else xIs0 = false;

and similar for the other end stop checks. (the == in the if is correct)
Look at = - Arduino Reference and http://arduino.cc/en/Reference/If for more info on when to use = or ==

I don't think this is the cause of the problem of xPos and yPos always reading 0, but it can't hurt to fix it.