Stephen,
Welcome to TU. As far as keeping the hook eye clean. There are a couple of ways that come to my mind.
#1 Take your forceps and grab the hook eye with them and then swish it through the powder.
#2 If you are getting that much powder in your hook eye, I will bet you are putting way too much powder on your jig. Thinner is always better as it will also reduce paint drips.
#3 Look into making a fluid bed, (PM me your e-mail) and I will send you plans, or use a powder paint sprayer.
#4 I personally don't like #1. That to me only works on small jigs. If you are painting bass jigs they are bigger and heavier. So what I do is find a drill bit that will fit easily in the hook eye. As soon as you put your jig through the powder paint, immediately take the shank end of a drill bit and push it through the hole until it comes out the other end.
There are many other ways I'm sure, as more guys will post their tips to help you.