If you are going to dive in and do the floor - and maybe (probably) stringers n transom, then my suggestion is start right off getting everything out. And by everything I mean motor, drive, transom/gimbal plates, upholstered side panels, cushions, seats, carpet - everything that can come out, get it out. Take pictures if you need to remember where they go.
It is far easier to assess and repair the structure of your boat when everything is out of the way of that structure. And it really doesn't take that long to put all that back. It for sure takes forever to work around something that will need removing by the time you finish the repairs anyway. And getting fiberglass dust in your motor isn't all that good for it. Nor your seats and cushions.
You can easily run your motor on blocks and rebuild your carburetor with it out of the boat. Easier in some ways than when it is in the boat. It is nice to have access to the motor while you do things like check compression, rebuild carb, inspect the exhaust manifolds and risers, and generally make everything perfect.