: while I was doing 150 grit sanding, I noticed some small pits in the epoxy.
: pin head size. Will the several coats of varnish fill these in?

Those pinholes are probably bubbles that were sanded in half. Varnish will not fill the bubbles. The varnish actually accentuates any surface irregularities. Now is the time to evaluate the quality of the finish you want versus the time to invest. Wetting the boat will give you an idea of the final finish, but water even hides the blemishes better than varnish. If it is good enough you’ll want to wash the sanding dust off with a little soapy water then rinse and proceed with the varnish. If you want to get rid of the pox you need to apply another fill coat and sand. If you want to remove any waves or crescents from the ROS additional fill coats will be necessary. The truest surface will be obtained with a fairing board. When you finally apply the first coat of varnish you will find blemishes that you can’t believe you missed. Then it is more sanding, filling, sanding and varnishing until it is to your liking or endurance. Then after varnishing if you really want to obsess you can polish the varnish. You’ll have a kayak that has the finish of a grand piano. Then you’ll take the kayak out and drag it across the rocks, bounce it off barnacles, beat it up with the paddle, bang it against docks, and drag yourself across it doing reentrys. It’s time for a sanity check, but then we are kayak builders and sanity is scarce.