I agree, this is exactly what it looked like when I get up close.
Thanks for the advice. I definitely seem to be struggling a little with the surface tension, I was just hoping there was a trick to getting them to fill. But I've spent enough hours on the build already, a few more trying to come up with a good enough solution won't kill me. Appreciate the help guys!

Saw a neat idea on KayakForum's Facebook page: try super glue.

"Robert Bolding: I use to repair chips in epoxy on electric guitars with super glue. the glue can be wet sanded to a high gloss finish and is perfectly clear. you might open up each bubble with a needle and fill with super glue."

I use it a lot for my inlays and assembling S&G kits. Thin super glue has much less surface tension than epoxy. Once you open the holes a few drops should penetrate quite well. Super glue is also clear and waterproof. How could trying hurt?