First its a FLOOR NOT A PIANO! Now lets go over your list.
1 day to sand and 2 days to stain and seal? Did he use Glitsa or Senteco? If he used Glitsa, No way. Senteco mabye if he stayed late. It is possible to buff, clean and seal in 2 hrs depending on size. "Circular sanding marks everywhere"? Are they edger marks or buffer marks? Did he use a Drum sander or a Buffer with a sanding disc?
You should not have been on the floor after staining! Cleaning up buffer dust and sawdust are 2 differnt things, Did you mention it to him?
As far as cleaning the counters, not his job. Paint on the walls...touch it up! What did you want him to do stop in the middle of staining to try to clean it only to make it bigger?
As far as the filler in nails/cracks IT WILL NEVER take the stain the same as wood. Hardwood will take stain diferntly, if it is a dark color it will be blotchy, If the heat was on in the house or has a heated basement the problem can be greater.
Just so you know, I had a customer who was so picky about the color, sand scratches, stain on the wall, that I had to redo the floor. Only to have her call at a later date to fix some scratches, Upon arival what did I find but her son riding his Big Wheel out the kitchen door thru the sand and back in the front door around and around on the hardwood floor.