[Hemi425HP]

That's the way the rule works. Assuming the pitcher is in the 9th spot (doesn't matter which spot but we'll use that as an example).
The bench player (in this instance a catcher) pinch hits for the pitcher. He now occupies the 9th spot in the batting order. The pitcher is now out of the game and can't return. He gets on base.
The 2nd bench player substitutes for the catcher, now he occupies the 9th spot in the batting order and the catcher cannot return to the game.

Once a player occupies a spot in the order, regardless of whether or not he's played in the field, that's the spot he occupies. The pinch runner cannot be moved to a different spot in the order since he's already occupying the 9th spot. You can keep him in the 9th spot and move him to shortstop and make other substitutions as necessary to fill the field positions. Easiest thing to do would be to drag your new pitcher into the former shortstops place in the order and then switch his position from __ to SS.