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How can I do substitutions by position number - i.e.. 9-1-9? When I click on a position, the substitution box displays names, not positions. How do I move players between positions if I don't know the names of the players being moved?

We do not quite understand this question. When doing a defensive substitution, you would tap the fielding position on the field diagram, then tap the player that is in that position. You need to know either the name of the player or the number of the player that is taking that position so you can choose them from the list of players available. If you don't know who the player is, then we would suggest asking someone or just leave that position empty.

When coaches make position changes, they tell the scorers by position. 9-1-9 is swapping the right fielder with the pitcher (position 9 moves to position 1 and position 1 moves to position 9).

When you tap the fielding position, you get the list of names, but not the positions they are playing. So unless I know the name of the opposition player who is pitching, it's hard to make the swap.

When you are on the defensive sub screen, it shows who is currently in each position, and even highlights the player in the position if you tap the button over the fielding position (i.e. tap the Pitcher position button, and it highlights who the current pitcher is, tap the Right Fielder position button, and it highlights who the current right fielder is). So if someone says RF and P are swapping, tap the Pitcher to see who the current pitcher is, tap RF and see who RF is, tap the pitcher name (now becomes RF), tap the pitcher again, and tap the old RF name and you have swapped the players.