I think I'd ask the installer to return and fix those pin holes. Three or four holes is not that bad, but 50 is too many.
As far as the damage to the wood floor, that's really up to you and the installer to work that out, but I'd at least bring it to their attention and see what comes of it. The floor should have been covered with plastic and/or paper to keep it from being damaged.
I don't know that I'd trust a sealer that is that old, considering the nominal cost of buying some more. If you really want to use it, call the sealer manufacturer and ask them about the shelf life.
_________________________
The top ten reasons to procrastinate:
1.