Yes you can delete unwanted bones by selecting in the set up room and clicking the delete key on the keyboard.

Yes it will take a long time.

Suggest that you also delete all IK chains using similar method. Select in hierarchy window, hit delete key.

Also suggest that you retain hip and the rest of the legs.

There are utilities available that will make the process much easier. One such is the PZ3editor http://www.philc.net/PZ3editor.php of which I obviously have a vested interest but I'm sure that others are available.

Alternatively you could make and apply a pose to simply hide the unwanted actors. By that I mean hide them from the drop down lists, not just hide them in the scene. Again the PZ3editor can do that.

Another point to note is that your donor CR2 may have some preset bends in it so to remove those:-

Figure > Zero Figure
Edit > Memorize > Figure

Hope that helps.