Have you primed the inside as well as the outside? If the inside is not primed, couldn't you fill the holes from that side?

I have seen everything from toothpicks epoxied into the holes and sanded flush to cab o sil or wood flour mix pressed into the holes and sanded flush prior to primer. 

From my experience, these are potential water intrusion points since they're not necessarily drill/fill/drilled, although you could probably argue that. 

If you aren't concerned about that, then you can just slather on some lightweight fairing compound and seal it behind the paint.

I've actually considered oversizing the holes then taping the inside, epoxy filling them from the outside to make sure the wood flour mix plugs the hole and is then considered a "feature" instead of a "bug".  This would obviously add considerably to the build time at this juncture...

Definitely fill the holes.  I learned the hard way: I thought they'd never show after 3-4 coats of paint/varnish, but they do.  Fill with a spec of epoxy with light wood flour and then sand them down before you Pre-Kote.

PS -- Like you, I realized after applying Pre-Kote.  Used a different epoxy to try to rectify it and then learned that this epoxy was harder than the Maas epoxy so they would not sand flat.  Sigh.

  I also made a late decision to fill the holes on my Skerry.  It would have been a lot easier if I had done it right off the bat.  I just dabbed a little thickened epoxy in each hole. Some holes required a couple of treatments.  A small cabinet scraper followed by 220 sandpaper ( I used emory boards) makes them completly invisible under the paint.   

   Thanks to all who have responded to my questions.  Also, it's nice to know I'm not the only one who's wandered into this dilemma. 

Doug Welch, did you sand off all the Pre-Kote before trying the other-than-MAAS epoxy?  If so, how hard was it to remove all the primer without sanding through the two coats of epoxy under them?  And when you found the epoxy filler wouldn't sand flat, did you just paint over it and live with it?

Hooper, same kind of question--by "late decision" do you mean after applying Pre-Kote?  If so, did you sand off the primer?  If so, how meticulous must one be in completely removing primer around each hole?  I think I've probably got close to 150 exterior holes to fill, which is why I'm still toying with the possibility of filling with something other than epoxy, something that would adhere over the Pre-Kote and sand fairly easily.  I know I might be shortening the life of my boat, but I'd be happy to get a useful 10 years out of it.

   I had not put on any pre-cote and actually opted not to use any.  I would think it would be quick and easy to sand off - and probably a good idea.  As soon as the color changes, you’re through.  Stop there and you shouldn’t bother the epoxy. If you’re filling with epoxy, it doesn’t matter if you sand through the original.  I doubt that a thorough removal is necessary.  I’ve seen pictures and videos of these boats a lot younger than 10 years old with  signs of water intrusion.  I would do everything possible to avoid it.  Once you get into a rhythm, 150 holes will go by pretty fast.

Hooper 

I am now building Eastport Prim (7/2018) and will paint the hull white.  I have plans on putting wood filling in the nail holes on the exterior before epoxy.  Any comments on this idea?  I have done that before and saw no problems.  (All boats will have water in it after each use.  Especially for fishing.)

Thanks in advance

NickL

Wood filler is not waterproof.  I would mix some epoxy and wood flour to make a boat builder's version of the same concept.

   I was trying to fine an easy way out.  I will go with epoxy and wood flour.  Thanks everyone.

NickL