wow, it sounds like you have way to much experience cleaning the interior haha! thanks for the advice, that is what I needed. Do you need a respirator to be able to work down there with all those chemicals?The hatch doesn't really fit snugly. If the hatch came up much higher, you couldn't get the top closed. Mine takes a good hard tug to pull the top closed over the hatch.
As for cleaning, go pick up a bottle or two of Mold Armor (sold everywhere). Remove wood and vinyl from the cabin, open up all possible ventilation, and just spray anything that isn't smooth (that's most of the ceiling). If you have padding on the ceiling you'll have to decide how to work around or replace it. Be careful not to breath in the fumes when working in tight spaces. After spraying everything, walk away for 10-15 minutes, then come back with the hose and spray out the interior. You'll be amazed.
Next, come back with a bottle of Wisk, a bucket of warm water, a big sponge, and a soft brush. Do your worst with that and rinse with the hose. Now you'll be able to identify the tough spots. If your boat it like mine, you've got perma-dirt ground into the gelcoat on the interior. An acetone-soaked rag helps quite a bit with much of that.
As for paint, there is nothing special about boat paint (on the interior). It's all about the prep work and cure time. I would definitely clean all smooth surfaces to be painted with acetone because you don't know what is on the surface (wax, etc.) You may find after cleaning that you don't need to paint, but you may still want to. Just take the extra day or two to get the prep work done right and you won't have to revisit the project at the end of the season.
I'm painting the ceiling of the interior in my boat, but am trying to decide on something to do with the smooth surfaces that won't just get scuffed up after a season or two. I'm pretty hard on stuff.
The thing I was most worried about the with hatch sealing issues was rain coming in. We quite frequently get some nice hard sideways rain that would blow right in!