I might be able to offer you a bit of advice learnt from experience.
If you are going to have active electronics inside a Jazzmaster type body & need to have a battery install within the guitar, by all means, get a battery rout done. I'd recommend it. Try to get it placed away from the existing cavities that are underneath the pickguard. You never know when you might be installing a buffer preamp or some other circuitry and if the battery is housed within the existing cavity space, you are losing valuable stowage area.
Take a look at how many screws hold the usual Jazzmaster pickguard in place, there's something 12 of them! If you are working on the electronics a lot, there will be wear & tear on those screws every time you take the pickguard off. Also, ensuire the screw holes are squarely placed to the pickguard, with the size of the pickguard you have a greater chance of it bubbling and warping if the screws are misplaced/ at angles to the body.
If you go for a Warmoth neck, most of their styles of necks have 22 frets - with the top fret overhanging the pickguard.
The original vintage Jazzmaster had only 21 frets and it made removing the pickguard just that little bit easier.
With a Warmoth 22 fret neck, there's the extra effort to slide the pickguard out from under the overhang & with pickups installed - that gets a bit finicky.
I've learnt this stuff from trial & error (didn't get a battery box installed & also had to have the 22nd fret cut off so I could remove the pickguard easier & frequently), so I'm hoping to save you some grief.