Let me answer those in reverse order - a pinch runner gets credit for everything he does - steals a base, scores a run - both go towards his season total.
Remember Herb Washington from the early 70s A's teams. All he did was pinch run. Pretty interesting career totals:
http://www.thebaseballcube.com/players/W/Herb-Washington.shtmlNo At Bats, 33 runs scored, 31 Stolen Bases and 17 Caught Stealing - as far as I can tell, he never played an inning in the field.
As for a courtesy runner, when I have been scoring travel baseball games (which is the only place I have encountered this rule), I have simply treated them as a pinch runner for everything except substitutions - that is they don't cost the original player or the runner anything in terms of their substitution rights.
Hope this is clear....
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