What is the best way to trim edges off of hardwood floor where wall was removed?
I would probably also go for the circular saw.
Make sure to use a variable depth circular saw and to set it to the same thickness as the existing floor boards, so you only trim them and nothing beneath them.
Then for the last pieces next to the wall where the circular blade won't reach you could use a hammer and a chisel to knock the last bit off.

As to the blackness:
Assuming you'll want to have the "filling" boards blend in with the existing floors, I'd advise to sand the whole floor and re-varnish/wax the floor.
The blackness is most likely dirt or a moisture stain that has built up over the years, when sanding give these spots special attention to make sure you sand them off but just make sure not to go too deep.
My parents have a rosewood floor and once every couple of years they sand the whole floor and apply new wax to it, afterwards it looks brand new.