Scrape the runs flush and a little sanding. The wood will not take any more because the hardned epoxy has blocked any chance of that. If you used regular epoxy vs non-blush, make sure you scrub the hull (or deck) with a scotch bright pad and water to remove any blush. Even a light sanding is good. Most people like to do the glassing during that window where you are guaranteed a good chemical bond. Normally that's as soon as the epoxy stiffens up.

Transparency is what you most want and S-glass is harder to get that from. It's also not necessary on a kayak. (unless you're really hard-core and plan on a lot of surf landings etc.) The common practice these days is to use 4 oz regular glass on the entire kayak wih a possible second layer on the abrasion area on the bottom. 5 or 6 oz is fine too.

I personally don't like tight weave glass because it presents wet-out and air entrapment problems.

As far as the blotchy look you're referring to?? I would wet it with water and see what you have, before you glass it-just to be safe and sure.