I've seen it done both ways for the board. Can't speak directly for KEE, but I've known a few people who have gotten boards swapped at no charge. I've also known people who just ordered a Shockwave board on their own. When you get the gun, contact Paintball Solutions and see what they'd want you to do on it.
Feedneck, I haven't had any functional problem with my stock neck. I'm going to replace it with the Empire Neck because I like that neck better (fell in love with it on my Resurrection and my Kryptonite Cocker), and I like the stub system instead of the one-piece neck body screwed directly into the gun.
The stock neck is a little "tall" for most people these days, but it's nothing like the old "smokestack" necks back in the day. I'd get the gun in, see if it's something that bothers you, and if it is, then worry about it. When I get the Empire neck, I'm going to put the stock neck back on my stock body and build a second Axe.