Just a wrap-up posting to note that since the old chain ran smoothly and passed the large/large and small/small test, what I finally did was to lay the new and old chains beside one another, link by link. This led me to remove only one link from the new chain and after putting it back on the bike, it works just fine and the position of the derailleur in both configurations looks perfect to me.

Thanks for everyone's patience and for all the great tips and links to relevant sites.