1. Last I checked, the S4 and the MS4 are the same. The S4R is of course different.
2. The S4 is a little bit higher than the other monsters by about 20mm. I am unsure of the 2003 Monsters in comparison to the older bikes but there is a height difference w/ the S4 that is in your benefit. You can set up the suspension to accommodate your weight and if you find that you need to you can raise the rear ride height a little for better handling and comfort. As far as options for upgrade you will soon find that this addiction sets in after purchase so beware!
You could have Corbin or Sargent make you a taller seat. My Corbin seat actually put me a little closer to the footpegs, which is not quite what I wanted. I guess I shouldn't have just ordered the standard seat.