Everyone goes through what you're experiencing especially on your first boat. On your second, you'll use more epoxy (or coats) to fill the weave and then some to allow for a level sanding without biting into the cloth.

Level it as best you can and varnish. You'll be floored what a coat of varnish will do once the kayak has an overall gloss. You won't see the small indentions. As you add subsequent coats and sand, You'll be coming closer to a perfect finish. In a few years! don't wory, the boat will look great.
I have my second stripper 7 years old, and I'm still leveling that one with with varnish and sanding. It's alled the no-load plan. Not much up front but lots of years of payments. I now learned to use enough epoxy to allow for the sanding part.