I've heard you've perfected the art of the sliding pup, Rob ... That would make sense especially on the 5er; the shortie could do with just two fixed pups. One up-front, one more to the middle, don't squeeze it too close to the bridge.
Don't be obsessed with a Gibson (parts) look, functionality comes first. Monorails as bridges are perfectly fine, for instance, let's go with the times.
The necks should have different woods perhaps. Maple on the shorty for a bit more bite, maho on the x-long scale for ultimate growl? Body for both: maho. Different fret board materials too. Why not a snappy maple board on the shorty? Ebony on the fretless.
Four controls, 1 x vol x-long scale sliding pup, 2 x vol short scale (each pup) and a master tone for everything, toggle switch for change between the basses, middle position: both on. That's all I need.
The shortie should have a high E (like in your design sketch), the 5er should have a double octave neck.
Two outputs for feeding them into different rigs? One of them functioning as a mono output for both if solely used.