M_Boats: Rot

Just pulled the bow pulpit off the M17 in the yard. There is a soft spot in the deck just aft of one of the deck flanges connected to the pipes that make up the pulpit. After cleaning the bolt hole out I notice that there is about an eighth inch of space between the underside of the deck and the top of the v-berth liner. I don't think I am going to get all the rot out with a nail on a drill bit. Am I looking at cutting out the liner below decks or removing the deck and cracked gelcoat right over the soft spot? I plan on painting the deck anyway as there are lots of stress cracks and crazing in the gelcoat. Seems like it would be easier to open the problem from the deck side. Any advice would be appreciated. Thanks, Tom B. M-17#258, 1977