If you have dry patches, that means that the vacuum is not uniform. Use a real breather layer (maybe $5 a yard from AC spruce -- save money by getting fake "fleece" from Walmart), to get a uniform vacuum. Or, perhaps the paper towels are wicking up the epoxy before you apply the vacuum.
An important distinction might also be that I used the dry micro method to prep my core. I applied micro and glass in two steps. First I applied the micro to the foam, let it cure, and sanded. I then applied my layups to the cured micro.
Why is this important? Well, if you coat the surface with micro, then lay up your glass, then vacuum bag it, most of the "pure" expoxy will get sucked into the breather layer, and the micro will get sucked up into the glass plies. This is bad, because your replacing glass w/micro bubbles, weakening the part. If you don't want to try the dry micro method, then lay up your parts with just pure epoxy on the surface--no wet micro. (Wouldn't recommend this for Divinicell / Blue Foam, too heavy).
I don't know if it makes a difference for you, but it worked for me.
My pump setup wasn't working properly, so I only had mayb 7" HG. Next time I'll try it w/15" HG. From what I've read, you don't want to go over 15" HG on most foam core substances. Between 10-15" is better.
For the blue styrofoam on the wings, even lower. Don't remember, but probably not more than 10" HG, max, or you'll start crushing the foam. You need a vacuum guage and bleeder valve if you want to do this right. They're cheap. $12 for the vac guage, you can use an air compressor bleader valve from Home Depot. All my fittings and hoses are from Home Depot, cheaper that way.
For single layer components (no core material) you can go up to 28" HG.
Lay up your parts very wet, put down peel ply, coat the peel ply w/epoxy so that there's no dry spots. Then lay down your breather layer (unlike paper towels, a real breather layer won't wick up the epoxy UNTIL you apply vacuum.) Then apply vacuum. I used a heat tent to speed the cure.