To get the full utilization of the hops, i would recommend leaving the hops in for the full boil. Some of the latest studies suggest that the hop oils and acids are nearly fully leached out of the vegetal matter within a short time, so you can probably get away with removing the hops after the wort starts boiling.
There is a little loss in doing a partial boil, but for as long as the hops are in the wort, you should be fine either way.
You can add the extract either before or after the fwh
The are no real specifications, it really comes down to how bitter you want the beer to be. BeerSmith does give you an estimate of the bitterness through the IBU model.
As with a lot of practices in brewing, how you operate your process is up to you. For a lot of your questions there really is not a right or wrong answer. You will just end up with a slightly different beer.