Hi Jim
It's true that everything like pickups, tailpiece/bridge/saddle slots should be lined up/ centered relative to the neck centerline, with distances relative to the nut maintained. Outside body dimensions should NOT be used as reference for line up. Outside dimensions do not come into play as far as scale length or pickup positioning. So creating a jig for referencing pickup and bridge locations relative to outside dimensions will not get you where you need to be.
Example:
One of the variables in a hand finished guitar or bass are the outside dimensions. The wood is CNC machined. So all things being equal, Program, machine and operator, the bodies will all be the same when they come out of the machine.
But the bodies are hand sanded and wood being what it is, very unique per piece, some bodies will require more hand work than others to achieve acceptable cosmetics. Now the bodies are no longer the same dimensionally.
Lets pretend that we just machined 3 bodies, all 3 required a different amount of sanding, now we have 3 bodies that are all a little bit different in their overall body dimensions. If you located the pickups, tailpieces and pickguards to the outside dimensions, each guitars critical components are going to line up differently relative to the necks centerline and relative to their distance from the nut.
If you ALWAYS work off the centerline of the neck and distance from the nut, the guitars critical components will ALWAYS be the same relative to these reference points. It will never matter how much hand sanding a body receives. You could have sanded 1/4" off the wings and it wouldn't matter. When it comes time to install the pickups and bridge assembly, you are going to use the NECK centerline and Nut for positioning.
(1st) Distance from the NUT to BRIDGE maintained to achieve correct scale length.
(2nd) Bridge centered to neck centerline.
(3rd) Pickups centered to neck centerline.
(4th) Pickups distance from nut established. Once the scale length is achieved with the bridge positioning, the pickup can be located from a dimension measured relative to the nut or the bridge.
(5) Bridge saddle slots cut with keeping an eye on string spacing on neck and pickup pole alignment. With the string spacing on the neck getting priority over pickup pole positioning.
From watching the videos posted one Rickenbacker construction techniques,
http://www.youtube.com/watch?v=NEuqgZzKxC4
it looks to me that the pickguard mounting holes are hand drilled just like the TRC. Same goes for the strap buttons and the bridge and treble pickup mounting screw holes. This is how I would do it. I would never lock myself into final component positioning by CNC machining the mounting holes.
The CNC just cuts the clearance pockets and routes in the body for the pickups, wires and control cavity. These are made a little bigger than needed to give the assembler some wiggle room to account for production tolerances.
When the pickguard (which the bass pickup is actually mounted to) gets installed the assembler can shift it around a little to get the neck pickup to line up with the neck centerline. Once that looks good, it could be held in place and the screws holes would be drilled into the body by hand using the pickgurad screw holes as a template.
Then the same for the treble pickup assembly. It's dropped into place, moved a bit to find it's center relative to the neck centerline, then once it looks good the screw holes are drilled into the body by hand using the chrome surround mounting holes as template.
From my experience, there is not much wiggle room for the bridge assembly. So the bridge would get installed into it's CNC machined pocket. But to compensate for any misalignment here we have the uncut bridge saddles. Once the bridge is screwed into position, you can install the strings and position them on the saddles to set string spacing and string alignment relative to the neck with the neck and hopefully the pickup poles at the same time(but pickup pole
alignment isn't all that critical, unless it's way out. adjustable pole pieces can help compensate for this, as well as balancing output between strings, and tone).
Mark the string position on the saddles, then cut your slots.
Hope that helps explain a bit about how it all comes together and what's important as far as references and locating.
I can't say for sure this is how Ric does it, but I have decades of machining and product development experience, dealing with complex mechanical assemblies, and knowing what I know along with taking apart many 4001/4003 basses it looks to me that this is how it's done. It's at least how I would do it.