Re: How much deck over the cabin do I remove?
I'm a real hack when repairing old boats so if you like 'pretty' - stop reading right here.
I would use a pressure treated board (on the inside) as a backing for the new rail, which would have rail posts made of pressure treated wood (or teak), filling the holes on top of the cabin with a fiberglass patch. I would drill a few holes from the inside (in the low spots of delamination) to drain the core so that the freeze damage is minimal. Trying to fix 'right' an old boat like that is usually not worth the money.
Be kind, for everyone you meet is fighting a hard battle.