The simplest suggestion I can offer you is this. Design your character names around the personality and nature of each character. I know that's not much help, but given that you're still in the design stage, you probably haven't solidified the personalities of your characters yet. Hence why you're having so many naming problems. I learned early on in my writing career that unless you truly know your characters, you can't name them properly.
The best way to prepare to write any story, especially if it's in a completely new and unfamiliar world, or contains new characters, is to literally live in the world until it's so familiar to you that you can see the story with a minimum of difficulty. If you can't see the story, and you don't know your characters intimately, you're just fighting a losing battle that'll eventually lead to you creating a substandard book.
Live your world until its second nature. Get to know your characters until you can express their every flaw and feature. Then once you've done that, share their story with the world.
Hope that helps.