get one of the kahler x200 series- either 2200 or 7200 (hybrid, pricier but better.) they're designed to mount onto the TOM studs of a les paul or SG- designed for a LP- no neck angle worries.
it's easier to adjust, easier to put in in the first place (with a scarf joint, at least), looks better, doesn't weaken up the headstock, doesn't take up any space on the headstock. lots of reasons.
peavey bravo 112, one of the countless 25W tube combos that peavey went through trying to find a good design. shame they settled on the valveking instead of the bravo, it's worlds better. it has a problem with the gain channel, though- it's really all or nothing. but sticking in 12AT7s instead of the AX7s really helped that.
it's not that overwhelmingly difficult to find poplar without mineral streaks- and if you can, it's amazing looking wood. i'm building a doubleneck next, and i'm using poplar with a top of some sort, not sure what yet. poplar is definitely harder than basswood, though.
with the body shape, i'd definitely go with a 4x2- the 3x3 would be too symmetrical for it.
i know they're cheap, but the crunchy PAFs would actually match the wood really well.
i'm liking the body shape- can't wait to see how it ends up!
The ZR is a great trem, the bigger problem is how thin the S is and how limited the pullup is. You'll run into the same problem trying to put a different trem into an S...virtually no pullup.
as long as the wood is all dried, i see no problems.
and if you wanted to do a 1/4" skunk stripe, you could cut out a slot the right depth for the truss rod before you glue the laminates, and do a couple wraps of tape on each end just so it fits snugly.
i'll have to see if i actually still have it, and if i do, if i can find it. it was a while ago, and it got stuck on my workbench, which has gotten cleaned a couple times. i'll go check.
EMGs have much lower output coils. this is then amplified beyond the point where passive pickups are. they do this for a few reasons, one of the bigger ones being less noise. i took one apart, it looked like it only had about half the normal number of windings.