Is there a significant reason for the end pours? Why couldn't you just drill the hull on each side, seal the hole edges and use a piece of PVC or Brass or Copper tubing, glued into place through the hull, with a nice fillet inside. I don't guess that this would work for you since you have already installed your deck.
Sounds like your plan for remedy will work just fine.

: Hey folks --
: Well, my planned Saturday launch of my Pygmy Goldeneye-HI didn't happen.
: Here's why: I drilled the end holes for toggles / tying the bow and stern
: to the car, etc., where I *thought* end pour epoxy existed. Apparently,
: though, there was enough of a leak in the cardboard dam that I used to
: block off the end pour area that where I drilled is just above where the
: epoxy settled to. I found this out when rinsing the dust and stuff out of
: the boat prior to putting it on the car to go paddle. I turned the boat
: over and Presto! Water running out of the bow toggle hole. Yuck.

: Here's how I propose to fix this; if anyone has comments or suggestions, I
: would be very grateful: 1) seal off both sides of the hole with masking
: tape;
: 2) set the boat upside down, with the bow on the ground and the stern
: elevated;
: 3) do another end pour, letting the epoxy just run down the underside of the
: deck to reach the bow;
: 4) let it cure, then redrill the hole in the same spot.

: I also plan on doing some poking and digging to check on the stern pour. I
: might just follow the above steps for the stern anyway, just to be safe.

: Does this sound like a reasonable approach to fix this?

: Thanks for listening!

: Regards,
: A Rather Deflated Bill Graham