If you look at the other W* thread I mentioned that I just bought a W* neck and an American Special Strat loaded body. The fit of the neck into the body was flawless. I was totally amazed that two parts could be manufactured by two different companies and that the fit could be so perfect, better than every F* guitar I've owned. And I mean perfect -- the fit could not possibly have been better. I have nothing to complain about, so I never bothered to contact W* customer support.
With that said, the neck was not flawless. The 22nd fret was installed at a bit of an angle, where it appeared that the tang of the fret bent sideways a bit as it was being press fitted. The result was that the spacing between the 21st and 22nd frets was not uniform on the E and e sides. I decided not to bother with a return, as I didn't think the problem was significant enough to be noticeable in practical use. So I can say that although the neck was definitely not perfect, I accepted it as it was and I didn't bother to contact C/S.
As good as the neck/body fit was between he W and F parts, I ended up returning the body, as it had a defect elsewhere.
My impression of W* is that they're good about allowing you to perform a return/rejection during the allotted time period, but once that time period expires your only option is a warranty claim, and warranty claims are up to their discretion as they build to their own standards. I hate to say it, but if their standards are not up to yours, you should have returned the defective parts right away. Now all you can do is argue with the guy who made your body that he didn't make it right. Chances are they're not going to be helpful. I suppose your only other option might be to seek help from your CC company.