I always saw the Jag-Stang bass as this, a Mustang bass with a humbucking pickup in the bridge, with 62' Jazz Bass type controls (Stacked Pots, volume/tone for each pickup, and a Jag-Stang type body shape elongated a little bit.
The tough choice for me is where the neck joins the body, should it be more like a Mustang Bass with the fretboard going well into the body, or with the 18th fret joining more like on the guitar.
The stacked pot idea is more from a Bass aesthetic, but if I were to go my way, it'd be one volume, one tone, and a 3-way switch, probably a slider acting as a pickup selector, located in a not as intrusive spot, like the treble side horn ala. Gibson Firebird IV 3-pickup non-reverse.