Overall, I think you generally know what you want, but you just wanted to have other forum members look over your "spec sheet" in case there's something you might not have considered.
I see three things you might want to think about before committing to a Warmoth bass with those specs:
- Consider if you really need a high mass bridge. To me, they just add weight and do nothing to improve tone. In my experience, they can sometimes actually suck tone off the high end. For a Jazz style bass, I'd recommend going with a vintage style bent plate bridge with the threaded saddles which allow you to set your own string spacing quite easily.
Brass nuts are, IMO, useless as well. They were all the rage in the 70's and 80's when everything was about "more mass and more sustain". But honestly, how often do you need that much sustain on an open note? And as soon as you fret a note, the nut is out of the equation anyway. About 1 out of 25 notes I play are open anyhow. And if you use a compressor, the whole sustain argument starts to become irrelevant. I'd go with a bone or a GraphTech nut...cheaper and lighter.
- I'd reconsider using the Duncan Quarter Pound pickups in your build. To me, they're some of the worst sounding bass pickups ever. I can't understand why people buy those things...scooped city. Why skimp on your dream build? Invest in some Lindy Fralins. Or even a EMG Geezer PJ set. But to me, $20 Artec pickups sound better than those Duncans, unless you specifically want that scooped tone.
- Body wood: Keep in mind that Warmoth bodies are generally up to 1/8th of an inch thicker than stock Fender bodies. I don't know why this is. Someone told me it has to do with the licensing agreement between Fender and Warmoth...but I don't really know for sure. So that extra wood is going to make the body heavier than a Fender body, all else being equal. But you mentioned chambering, so that will help. I don't like mahogany for basses. Not enough bottom for me. It's fine for guitars, though. I'd go for ash, alder or even (*gasp*) basswood, since you're going for a flame maple top.
- Your side mounted Strat-jack idea sounds interesting but for the sake of simplicity, it might be easier to go with a conventional top-mount for that, like Fender does on the Aerodyne Jazz. I think it looks cool. But if you have it figured out, then go for it. Hopefully Warmoth can accommodate you with the special routing you might need.
Keep in mind I'm just pointing out things that stood out to me. You may or may not agree with me on some or all of these points. But as a session and touring musician with 25 years of professional experience and who's played a lot of different guitars and basses, I'm just trying to give you honest feedback based on my own experiences. I'm thinking this is what you requested based on your original post. No matter what you decide, I really hope your build turns out the way you want and that you end up a killer bass that inspires you to play great music. Good luck and welcome to TalkBass.