Hey Zoo Keeper,
The difference in position of the bridge pickup, resp. in the JS being closer to the bridge, will result in a thinner or at least less bassier sound - at least in my experience (assuming you set the pickups to the same distance to strings, using the same string gauge, overall as similar conditions as possible).
I think nowadays we all know that tonewood does not, or better: CAN not make a perceivable difference in sound on a purely electric guitar, and since both of your guitars have at least a very similar vibrato, we can rule that out too. 22 frets vs 24 frets also doesn’t make a difference, since both guitars have the same scale length.
We all know that neck pickups in general sound much fuller and bassier than bridge pickups: because of the position in relation to the bridge.
I have a guitar I absolutely love, and its bridge is around 5-8mm closer (depending on which saddle I measure) to the bridge pickup compared to my EBMM Axis (Super) Sports. The Axis Sports still sound quite a bite fuller and bassier using the same bridge pickup and adjusting everything as close to each other as possible on both guitars.
I ended up using a Tone Zone in that other guitar and I absolutely love it, and it also balances really well to a low output PAF-ish neck pickup there.
So I‘d recommend a Tone Zone or Air Zone. Also a AT-1 might work well there, but I remember it being a little soft in its attack, almost being a bit spongy (had it in my Axis Sports as well).
Keep in mind, that TZ or AZ won’t sound too dark or dull compared to many other guitars, because a position closer to the bridge balances things out quite well. At least, that’s what I experienced.
TBH, I didn’t expect the 5..6..7..8 mm to make such a difference, but well, it did.
I think that most folks don’t take this into account (I didn’t either!), when evaluating the sound of pickups.