As for the leaks. Rebed the ones you are sure of the start rebedding hardware near the leaks and work your way outward from the leaks. While water does not run uphill, it will follow a wire or such downhill for a long distance before showing itself inside. Just be patient and think eliminate sources 1 by 1. You can do it.
Second alternative is to rebed everything. That is what I did and it is great to have a dry boat.