Your image doesn't show up in the post. But based upon what you have written, I would advise you to consider adding one more complete coat of epoxy so that absolutely everything is protected from water penetration. Then, be very cautious in the amount of sanding you do before varnishing or painting. Wet sand by hand with 320 or 400 grit paper. I know that the manual says to get everything a uniform cloudy gray, but I think it's more important to have a protective finish than a show-room finish. Sand out any drips and dust particles, but don't sand through to bare wood anywhere! . . . Just my 2 cents.

   Thanks for the reply.  Sorry about the Pic.  I put 3 good coats of epoxy and 99% of the boat is fully covered, so I am only talking about some very minir spots.  I agree with what you said about the light sanding vs taking off the epoxy.  I may try and apply epoxy to those spots and lightly sanding them.  I was nervous about the inside because the book said that varnish would not stick to unsanded epoxy but I supose a tiny spot would not cause a big problem.  I think I over obsessed about the sanding.  

first, everything needs to be coated in epoxy to prevent water penetration.  so any sand-through, even minor, needs to be addressed.

that said, a way to fix minor sand throughs is to use a spreader/squeegee and apply a very thin/smooth coat that is feathered into the adjacent hull.  then when you sand....you can lightly sand the feather area....but you dont really need anything other than a light scuffing of the sand-through area becuase the overcoat of epoxy went down very smooth.  two or three little coats like this often take care of sand-throughs very efficiently.

this is a little bit of a technique thing that you will develop after doing this for a while.  when dealing with sandthroughs, its often common to repeat the sandthrough becuase you create another bump that, in your attempt to address, creates another sand-through.

   Thanks hspira...That is helpful.