Although you have gone through a lot to get where you are now, you're not in that bad shape. Sand first, then epoxy. Sanding not only levels, it cleans as well (blush) which is why you usually get pockets in epoxy.

As for your bare wood giving you pockets, It probably had some kind of contamination, oil, wax etc. which caused the pockets. Once a surface is sanded clean, you never get that.

Many people use non-blush epoxies now which really helps with all of that. (but you don't have to)

When you wet out glass, epoxy is in the depressions in the weave and on top of the threads as well. It's good to give it a light sanding taking off the epoxy thats up on the strands. Then use some ammonia and water and scrub the surface with a scotch bright pad - hard - cleaning any blush that's in the depressions.

If you know your epoxy, many people give subsiquent coats within the window of adhesion (specified by the manufacturer) Basically the sooner the better.

Since you've had problems, I would mix a small batch and watch it for a half hour or so to see if it seperates before I start coating the whole boat.

You could user a thickner like graphite, however with 3.5 oz cloth as you used, it's really not very rough and not necessary. With really aggressive cloth, some people will squeege on a filler coat - but not usually for kayak builders who desire tansparent sheathings.