Re: nail holes in flooring
There are tens, or hundreds of thousands of homes with just that situation. My current and last houses included.
Personally I have come to accept that part of the character of an old house is the fact that some maroon thought it would be a good idea to cover the finished wood floors with wall to wall carpet.
To fill the holes you could use a sawdust and glue combo from sanding your floors, or you could just sand and refinish while ignoring the holes, which is what I have seen the most of.
Will the little black marks annoy you that much?
It's this old house, not this built after your dad was born house.