I used a syringe with a 14 to 20 gauge needle or angiocath depending on the size of the opening. Thickened epoxy enough to fill but thin enough to push through the small needle. It took some time but I was able to seal seams and stitch holes. I also backed up the holes with s piece of tape. I probably had 10 to 12 holes on a dory. I found this very useful for filling low seams. Fortunately I had access to these supplies because I work in the medical field. Using a putty knife only superficially filled the holes. I went with a complete fill. I probably spent 3 hours filling and refilling. But I did get a completely sealed boat 

   Thank you for your suggestion.  Unfortunately, I have no access to syringes, but I do have access to tape.  I am thinking about putting tape on the outside of the canoe, turning the canoe on its side, making a small batch of epoxy, filling the holes, and letting gravity help.  I will have to do this twice, to get the port and starboard sides, but I have to do what I have to do.

 Gravity may not help enough.  Bubbles will likely form in the holes.  Then when you clean up your epoxy fills, you may find that you still have holes.  You could probably inject epoxy with a plastic disposable squeeze bottle.  If not, you may be better off making it a little thicker and forcing it in with a plastic puddy knife (without the tape)  

Hooper Williams - Brevard, NC 

   I had an unfilled hole or two on my NE Dory. Finding them is one justification for splashing the boat a bit with some early rows and sails before moving on to varnishing and painting. (Of course, impatience was my real reason for launching as early as possible.)

I mixed up a tiny bit of epoxy and dribbled it in the holes and may have put a bit of tape on the outside. I did not worry about completely filling them with epoxy. If I had to worry about that, I would have had to inspect all the other wire holes on the boat!

Thank you for your replies, they have all put one or another of my comcerns to rest.

The holes that were completely unfilled I have used your suggestions and materials I had on hand to fill.  I first tried cutting some unused fiberglass into small shreds, mixing it with epoxy, then using a wire to pack it into the holes.  That worked, but was a bit annoying.  I then found another hole that was unfilled, and after cursing at myself for not seeing it earlier, I looped some fiberglass threads around some monofilament fishing line.  Pulled the glass loop through the hole, put some epoxy on, worked the glass back and forth in the hole until the epoxy was in, then left it to set.  Easier and it looks well plugged.

Maybe I will take the boat out to a local lake and give it a dip before I go on to finishing.

Thanks again!