I suppose I should finish off the dorade box blog. They're all back together and I'm waiting for the proof that the fix worked. Seattle's rains have returned, so a few more weeks will probably wash away any doubts. You don't say where the leaks are showing up or why you think it's around the boxes or the mast.
On my E38, the dorade box and the open oval-shaped space in between have plywood floors that are resting on the inside fiberglass surface of the house top. At least the large center section is connected to the rest of the house top core, as far as I can tell. I took out the rotten plywood to the edges of the glass that was in there. Then I poured in the CPES, which is like water, and let it cure for several weeks. Later, I glassed in a new floor (two small pieces of Coosa board) and that seems to have taken care of the center section. I also made sure the drains on the aft side were clear. I haven't painted the interior, but might do so with an exterior latex.
The two actual dorade boxes let water in via the bronze rings and possibly via the dorades themselves. I presumed their plywood floors are in contact with the deck core, but that is harder to prove. I cleaned the interior of the dorade boxes and the floor with rags and solvent, a light sanding and then vacuumed them out as well as I could. I used CPES to soak and seal the wood floors, probably poured in 12 ounces per side. I came back in and used regular epoxy over the floors to fill in the gaps in the plywood, where I could reach with a small brush. I did not take out the tubes. They looked ok. I had the headliner down in the area and there was no water leak where they came through the cabin top. I also removed the bronze rings and cleaned up and re-bedded them at the end of the project. I had to remove them to get my hand inside to clean and seal.
I also sealed one obviously leaking bolt on the mast ring. I have 17 more to go in the ring. I put a bead of sealer around the mast ring on the house top. I used 3M 4200. I also re-bedded the bases of the steel tube tripod that protects the dorades. There were certainly problems there. To re-install, you have to prep all the spots first, put the bases on the tripod and put them all down at once.
One last thing to consider. When I re-position or remove house top hardware, I seal up the unused surface holes on top with epoxy and all that. On the bottom, I leave the smaller fastener holes open to the core. These are the tell-tale weep holes that will warn you of wet core from above. They also permit the core to dry out during the hot summer months. If your boat has things like plywood pads screwed to the underside of the house top or decks, these screws probably get into the wood core. The tiny staples used to nail my boat's flimsy foam insulation layer to the cabin top often penetrate to the wood core and will warn you of core wetness. The problem with all this is the water usually runs down the headliner to the edges and stains your wood trim on the way to your cushions. So, there is a trade-off and you'll have to decide which is acceptable to you. I have some stains to deal with, later, when I get to the headliner and interior beautification project.
I hope you find this helpful.