Owner of a small Boston Whaler for over 40 years now. Have it in dry storage waiting for time. So, I've done many years of reading on the topic. As you know, BWs are foam filled. There are only 2 ways to correct soaked foam and only one is foul proof and safe. Generally, an undesirable option. Removal of all foam is the first. Drying is the second which, is so so.
Depending on the encapsulated chambers, on BWs you drill 2" holes at the low points and high points of the foam areas and prop up the boat to dry for a year in a covered spot. My little baby whaler has been sitting for 18 months now.
If you have water weeping out, you need to know a few things for safety. The original weight of the hull, weight as outfitted, weight added when the modifications were made.
Current weight, weight after holes and Drying and weight months thereafter. One fellow restoring a 21' whaler lost 600lbs of weight after drilling core holes and propping up the hull for 18 months. He ended up pulling the decks, stripping the foam and rebuilding it. Determined I guess?
Soggy hull makes glass go bad too. So, not something to take lightly in a bigger and modified boat I'd say.