Are you saying you have 3/4" scuppers? That's what I thought. Mine appear very small also. I'm partial to at least 1 1/4" scuppers in my boats and thinking of changing them out if they are too small.
When you refer to the board that holds the liner up, do you mean the wood you find under the cabin top, up against the hull? In the aft cabin this runs along the upper inside cabin where the pan liner meats the headliner. If this is wet, as mine was, I am guessing its not from the hull-deck joint. Its from the windows. Water leaks into the cabin top via the window seals and runs down the liner to the wood backing plates. The portholes are not glassed very well from the factory and usually rotted out. My guess is if you pull the head liner you will be horrified.
You're goign to want to look at this thread to see what you're in for:
A27-Beckson Ports Window leak Thread
To avoid "overwhelming syndrome" --Don't do this until you have completed your scupper and cockpit sole project.

I suffer the same feeling every time I climb on the boat. Its gutted and 15 projects started at one time. But IMO its better to do everything at once than to try and fix things piecemeal.