My question would be...."How did the tell-tale traces of paint end up in the wood grain?"  If the boat was  glasscloth covered and epoxied, that should have pretty much precluded paint filling the grain pores.  What color was it painted?  Are you sure that someone didn't sand through the epoxy and cloth and the epoxy dust is what you are seeing in the pores?

Good question.  I'm wondering about that myself.  From what I can tell, the top of the boat was not glassclothed, but only epoxied.  There are traces of light blue paint which seem to have been sanded smooth with the surrounding areas.  Rubbing your hand over the surface you cannot feel the paint.  I have sanded a couple of these places hard--harder than I would like--and the paint came off but then there is a slight depression in the surface.  I'm thinking of sanding all the paint off, then apply fresh epoxy, then sand and varnish.  It is going to take lots of work.  Oh by the way, I do have some leftover PeelAway paint remover that might take the paint off.  Thanks very much for your response.  

I would advise against using old remover.  An old  finisihers trick for removing paint  from pores is to recoat the entire surface with a thinned down coat of shallac. After it dries  it can be re-stripped (not sanded) and it will often pull the remaining paint from the pores.  Usually pretty effective dependent upon the type of original paint  but it is a lot of extra work.  Just depends upon how intent you are on a "clear" deck.  There are some good commercial removers out there that are stronger  an more effective than the BigBox or paint store varieties but you'll need to seek them out from professional finishers.

These commercial removers you mention, do they have any effect on epoxy?

Some of them can but mostly if you use the types formulated for aircraft finish.  Commercial (industrial)  Methylene Choride - type removers will take off paints & enamels but will mostly rinse off of the epoxy with little or no dulling of the sheen.  Always experiment in a small un-noticable area.