As you say, the water could be coming in somewhere else and running down the coachroof.
You'll see when you get the internals out, but most common/obvious places to check are:-
Windows - the foam gaskets go hard and crumbly and you can get water leaking in behind the window (most of mine did this). Cure it by removing the window frame, cleaning off the old foam, and re-seating using Abromast Butyl sealant.
Genoa track - if you have bolt leaks here, try Capt. Tolleys.
Get someone to put a hosepipe on the boat while you're inside. You'll soon see where its coming from.
Best of luck
Bob