Keep doing the soap thing until it stops leaking. One thing to remember is that when you put air into the hull that flex you're seeing in things like the centre cases may actually be closing holes. This is one of the reasons (aside from damaging the hulls) why you don't want too much pressure.

If you do fix this "plugs" in the transom:

1. Remove existing plugs.
2. Fill holes with plasticine
3. though inspection ports apply glass to inside.
4. dig out plasticine and clean well with acetone or similar.
5. Fill hole with bog.
6. Fair and paint.