A couple of things, first I've never used Warmoth products. However, I've used USA Custom Guitars bodies and necks, and I can literally pick up the body with the neck without the neck being bolted on. Second, I would suspect that the Warmoth neck is fine. I'm willing to bet that Fender allows looser tolerances than Warmoth does. Third, most folks believe that the best neck joint comes from having no paint at all in the neck cavity.
Where does that leave you? Well, where is the slop in the joint? Is it on the sides? You may just try making a very small shim.