In working on the attic I picked up a new tool: an oscillating multi tool
. Some of the boards in the attic that needed to be replaced were right on the edge. This edge has a 2x4" nailed on top of it and makes the nails on the edge of the board inaccessible. These boards would have to be removed in order to be replaced. The oscillation tool with a duel-metal/wood saw blade was just what I needed. I was able to cut off the old nails and pull the remains of the old boards out. Then I could replace it all with the new floor boards I cut. Some of the nails were a more stubborn than others but I was able to remove them all.
I was going to replace the missing cellulose insulation with more cellulose insulation, but the guy at the home improvement store said you really need a machine to blow that insulation in. Instead he recommended using loss fill fibreglass. The price is about the same, but you can break it and fluff it by hand. So I picked up a bale of that and soon had all the rafters topped off.