The necks at Warmoth are very good, but I’d still go with Doug at soulmateguitars.com. He is pretty easy to work with and encourages people to be creative in their design. You can pick out the layers of wood, create you own headstock shape, get a custom radius on the neck, etc. I also had him put a slight V shape on the back of the neck and abalone dot markers, at no additional cost.
I didn’t have Warmoth cut any of the control routs. I ended up putting the 5-way switch exactly where they would have, because of how the wood extends out to attach the cover plate and the deeper rout required. Be careful, I had a bit of an issue with them on the cost of finishing. They tried to tack on a $50 upcharge because it was an exotic wood. It took some phone calls, but I got them to waive the charge since it wasn’t listed anywhere on their website and didn’t come up on the checkout.
If you have Warmoth create the body from scratch, rather than pick one from stock, you can tell them not to cut anything for the bridge if you’re going to go with the Jack-of-Roses hardware. (Put your order in with him on the brass right away!) If you want to go with three humbuckers, they’re offering a “Nalls Mod” for $65 which puts them closer together. I didn’t do this since he had a pickup ring to fit the regular spacing.
Good luck and have fun!