The first cut is the hardest...
The only reason to do it from the outside is to the preserve the finish. If you are going to paint, then you might as well work from the outside where access is better; this makes the job much easier.
As far as the work on the bottom goes, I would suggest drilling pilot holes to assess the range and degree of core saturation. If the core is soaked, then just cut it all out and replace it. Core and fiberglass are cheap and you're not going to be doing yourself any favors filling and fairing all of those holes.
I have tried repairing wet core a number of ways on a number of boats and the one constant I've found is that it's quickest and easiest to just cut and grind the old stuff out.
As far as the cabin top goes: it will be easier to paint but the rest of the job will be more difficult. Not impossible, but harder.
There are two ways to go about it, assuming you go from the inside. You can either cut away and discard the old inside skin or you can try to preserve the old skin for re-use.
If you do try and re-use the old skin, brace it very well. The downside here is that it is hard to get a very good bond. Use a lot of thickened epoxy (thicken with colloidal silica) and press the skin back in place and brace it very well. Make your braces ahead of time and have them ready to go. You will probably have to hold the skin in place with your hands until the epoxy kicks; it's very hard to keep it in exactly the right spot and install the braces properly before the epoxy kicks. Place wax paper between the brace and the work surface.
After the old skin cures in place, grind the seams and lay in 2 layers of 10 oz. fiberglass tape. Sand, fair, and paint.
Depending on how good you are with fiberglass, it may be easier just to layup a new inner skin. One or two layers of 1708 biax cloth and an outer layer of 8 or 10 oz cloth is more than enough. This is a PIA to do on an overhead surface. Wet out the surface well before applying the cloth and use a lot of resin on your first cloth layer.
Use small pieces of cloth and hold the piece in the center until it will support its own weight. Abut the seams; if you overlap them, you'll have a lot more grinding and fairing to do. Then, on the second layer, make sure the seams don't line up with those from the first layer.
Let the 2 biax layers cure overnight. Sand well and then apply the outer layer of light-weight cloth, the purpose of which is to make finishing easier.
Also, when you're working overhead, strands of cloth will hang down all along your cut edges. You'll be tempted to deal with them while you're working with the wet cloth - just leave them and cut the cured stringy bits off later with a cut off wheel on a dremel or a similar tool.
As an FYI, white vinegar is effective at getting epoxy off your skin and is healthier than acetone. Have some of this on hand. When I recored my foredeck, a large drop of epoxy fell between my tyvek hood and my goggles and landed on my eye. I was in my anchor locker at the time - that really sucked.
