Why don't you take a picture of the offending tooth? It could be that one got bent.

That article is pretty good - bringing me back up to speed with some changes since I left - at that time you simply replaced the chain when you got a new freewheel and did not expect a new chain to work on an old freewheel (which could also create skipping problems - particularly if the chain had been allowed to rust on the bike and was replaced to sell it) - but that freewheel does not very worn. I can't recall ever measuring a chain - it was just a given that you replaced it with a freehwheel change and those wore out quickly enough.