Put on a thin sealing coat of epoxy, and let it set up before you apply the glass. It will either fill the cracks, and harden inside them, preventing starved areas when you apply the cloth , or, it will completely drip through, and show up on the inside as tiny stalactites -- with each one indicating an area you'll have to give a bit more attention to.

Use a paint scraper to remove the soft epoxy resin globs from the inside while the resin is still a bit soft (within a day or two) and place a dab of masking tape over the offending gap. If the gap is big enough, plug it with a toothpick or a toothpick sized piece of cedar from one of your waste strips. Otherwise, you can fill the gaps with epoxy that has been thickened with some fine sawdust from the sanding you did when fairing the hull. An ounce of resin should do for all your gaps. Yhey shouldn't need more than a drop or two each. You can leave the filler a bit above the surface. After it sets up it will be just a few seconds to sand such small areas flush.

As a final prep step, hand sand the whole boat to remove highspots, and drips, and to slightly roughen the epoxy coat so that the coat that goes on eith teh glas has a good bond. Rinse off the sanding dust and you'll have removed any amine blush, too. You don't have to go too wild with this sanding step. Extra fine paper is foolish, and using a power tools is a waste of power. A block of wood with a piece of sandpaper wrapped around it is just the thing. Wipe this over your boat like you would use a sponge on your car when you wash it. No pressure needed, but you want to cover the entire area. You'll be rewarded with an ugly smear of fine scratches from the sandpaper. The next coat of resin will fill these in and turn them transparent, while using them for a strong bond.

use squeegees when applying the resin and you'll be able to keep the seal coat light, and also put on the minimum resin when you apply the glass. Since the wood is sealed you won't get resin soaking away from the glass, starving it, so don't let any puddle up.

Hope this helps

PGJ