Prepping the bass for future Series II electronics is $1300 additional. This includes making the body thicker to actually hold the electronics, mounting the humcanceller pickup, making and mouting the two additional backplates, shielding the upper body half, mounting the 5-pin housing. We don't drill for all the future holes, just leave room so they can be drilled.
Also, the bass will have to come back to the factory to have the electronics installed. While the prepping for the future electronics makes the job easier (and possible), there is still calibration work once everything is installed that must be done here. Take this into consideration when making your decision.
This decision will have to be made quickly, since a neck made for your original specifications will not be thick enough for the Series II body thickness.