Well with a bit of ingenuity and lateral thinking, we've solved our first two problems.
1. We decided to swap the position of the switch and the volume pot, so that the switch is now in the middle, a la the EX-1. The switch now has a horizontal orientation, yay! We enlarged the middle hole so that the switch barrel fit, and now it comes through enough that the locking nut can bite, with the washer on.
I also 3D printed a grommet for the pot to fit snugly in the oversized hole where the switch was supposed to be.
2. With a gentle bit of hand flexing, the jack plate is now concave and fits flush to the body.
Unless anyone thinks that doing so would lead to instantaneous death or some other dire consequence, we're going to go ahead with the bolt on neck.