Its possible it was extra, as long as you replaced what came out with new ones, it should be ok. As for cleaning inside the tube, its not really needed if you kept it clean.Rod came out easy, just as you described, took it appart, cleaned it up and replaced all the seals/o-rings.... but there was one large o-ring left, no mention of it in the manual, could it be an extra in case a different piston used it? Also I can't really look inside the tube the way it is , could it go in there? If so there is no mention of it in the repair manual. How about cleaning the inside of the tube should I be concerned with that?
It will not go indide the tube, the tube is just a tube with a cap on the end. The seals only go on the piston and the gland.