Shape a tightly fitting neck pocket for maximized resonance of sound between neck and body. Define alignment of the vertical axis and establish the neck position to measure the scale for your guitar.
Attach neck and body. Then thread some fake strings onto your soon-to-be guitar and carefully measure the scale from nut to saddle. Now mark the placement for your bridge.
Depending on the type of bridge you buy, you may have to quickly drill 6 holes through your body and attach string ferrules. NO, DON’T ATTEMPT TO DO IT QUICKLY! Do it properly and unlike me…
On a side note: Several online shops sell routing templates for most common guitar parts. But it is fairly easy to make them yourself - even without a CNC milling machine.
Align and fix your templates to the body and carve a smooth couple of routes to create the remaining pockets. Don’t enjoy the results of your work too much, the wood you uncover will be filled with hardware anyway - a small price to pay.
Finalize the body sculting process by digging some tunnels. This includes both a socket for the input jack as well as channels to run wires towards the control cavity.
Don’t rush into implementing your design. After finishing the body, it’ll be the perfect time to take a step back and evaluate options for a custom headstock shape and hardware color accents.
As the name already hints at, the headstock can be considered the face of a guitar. Once the body is dressed, go ahead and model it. While you’re at it, why not embed a sheet of skatewood for good measure?