Re: soft spot repair
I will start with the obligatory: "Pics, or it doesn't exist."
Because you've found a couple of places that are soft relatively high on your vessel, I suspect you'll want to now begin a careful analysis of any wood at the lowest points -- bottom of transom, motor mounts, base of stringers in bilge, etc.
Fixing the covers would be amongst the easier repairs if the outside skins are intact. The techniques will be similar to those you may have read about in transom replacement threads: removal of the bottom skin and rotten plywood core, grinding and prep, peanut butter of replacement wood to the empty hatch cover, and laminating new layers of cloth and mat.
Post some pics and the peanut gallery will weigh in.
