If the stringer tops are cut into and not correctly capped, then they are a lot weaker than stock. It is hard to tell from the photo. If they have been hacked, then you will want to address that. (edit: you said they might have been raised already?)
If done properly, you can grit blast fiberglass rather than sanding for prep. But just like sanding, there is a lot of vacuuming and other prep. But way faster for rough/uneven surfaces.
My suggestion for raising the floor is to use pultruded fiberglass tubing rather than 2x4s. It is straight, strong, light, inexpensive and rot proof. And you can use for wire routing. I hold my fuel tanks in with it where rotten 2x4s were.
http://www.mcmaster.com/#fiberglass-hollow-bars/=oimc42
I have a different opinion about how much foam the boats need. But it is a matter of philosophy. Or maybe bad math on my part. My 20 footer has enough to not sink, even with a full tank and a gaping hole. It is a lot of foam. A pretty unlikely scenario.
I think next time I will go with block/sheet polyethylene or polypropylene foam.