I'm not sure how phase works with the Alembic pickups. Strat tones for combined pickups are always reversed so you get that hollowish tone. You'll probably have to specify this as well, and maybe need a mini toggle to reverse the center pickup to allow you all the possibilities if you want them. I'm not sure if this is even possible with the dummy pickup circuit unless maybe you assign one dummy to the center pickup and reverse it when the pickup reverses. The other dummy can work with the bridge and neck pickups in a standard series configuration.
Series instruments almost universally are dual pickup (I've never seen a one or three pickup model, but one may exist) and the 5-pin connector carries the pickup signals separately. Have you considered whether you will require a DS-7R and a 7-pin jack and cable to carry the three pickup signals separately or, if not, how you plan to separate them? I don't know if there is even such a thing as a 4-conductor 1/4 jack, so who knows where you're going to end up there.
Your tremolo is going to have to go through Mica for approval. I know I have never seen an Alembic tailpiece turned into a tremolo, so you may have to look at some OEM parts for that purpose. Any tremolo that goes through the body in the Fender style is going to impact the value of the neck-through design since it will sever the neck at that point and the tailpiece will be less solidly anchored. Don't know if the impact will be detectable, just that it is worth considering. I believe Alembic has used Floyd Rose, Kahler, and Bigsby style tremolos in guitars in the past. There is also the Skyway that is, I think, in the process of being installed for the first time. I don't believe any of these involve cutting completely through to the back of the guitar.
The extra pickup on a Series instrument is probably going to add quite a while to your lead time. You can probably get a guitar that looks like a Strat using the middle pickup as the dummy in a reasonable time, but adding the circuitry for a third live pickup is probably going to require some extra bench time for Ron. Again, not guaranteed, but something you'll want to clarify with Mica before you move forward.
-bob