...Another place to look for leaks are the cabin top handrails if you have them. After alot of searching on my boat, they proved to be a source of several leaks, and they will travel between the deck and the liner until they appear somewhere in the cabin.
Me too, I had a bad leak at the top of a portlight, except it actually came from the cabin top handrail and ran down above the liner till it hit the portlight, then ran inside the cabin.
Brilliant idea... just don't ever, ever, ever use red! Red chalk stains! It's banned from my jobs except for rough framing.
Red chalk doesn't so much stain, it's actually is and is supposed to be permanent red ink. Very useful where it will be covered but you want the line to stand up to traffic, rain etc. For instance, laying out roofing.