Paul, it wasn't my intention to scare you out of your plan. The plan you have for your custom sounds like a great plan that would produce a wonderful and awesome bass.
In my opinion, the Alembic low-pass filter and Q setup is FAR more flexible and versatile than bass & treble controls. IF you had to choose between them, the filter/Q setup is far superior.
My point was that you DON'T need to choose; it's not either/or (unless you want it to be)... you can have BOTH.
There are several Alembic basses that have BOTH the filter/Q AND e.q. controls. First of all, the Distillate, Europa, and Rogue all have a single low-pass filter with a Q switch AND 3-position boost/flat/cut switches for the bass and treble.
Several club members have customs that take it further and have variable knobs augmenting the filter/Q setup. Check out the Custom Archives. Understated Elegance is a Series II bass that ALSO has individual bass and treble knobs FOR EACH PICKUP; my custom 8 Strings of Power also has individual filters, Q switches, AND bass & treble knobs for each pickup. The East Meets West bass has bass & treble knobs supplementing the single filter & Q switch; and if you look up Rory's Custom Bass in FTC, you see that it has Anniversery electronics (individual filters & Qs) PLUS individual bass & treble controls. Also, you can see Shim's custom bass is getting a master set of bass & treble knobs to supplement the individual filters & Q switches.
My experience is that I love both options. I want BOTH the filter/Q controls AND bass & treble controls... and want both types on my Alembics. I really enjoy and use the tremendous versatility that my bass offers by having both sets of controls, and I would never consider an Alembic with either/or. But that's me.
My point is, if you can afford a Series II, an extra couple hundred for the bass & treble toggles or knobs is a drop in the bucket. If this is your dream bass, and you have a concern about it, it wouldn't cost much more to add 1 or 2 sets of toggles or knobs, and they can do it -they've done it before, for me, and several other club members. If you want bass & treble controls, why not get 'em?
As far as the ebony goes, again, I didn't mean to scare you. I'm a big proponent of Ebony in the neck. It's indescribably awesome. But it is also expensive and heavy... and the Series electronics are also notoriously heavy. You should be aware of this in making your decision.
Mica told me that they currently recommend just 1 or 2 (Ebony) laminates in general, and that just one or two will provide virtually as much of the effect as a full complement (every other laminate). My understanding is that each Ebony laminate adds about a pound to the weight. Maybe this wouldn't matter to you; or maybe it would. Only you can say.
There's nothing wrong with your plan. It's a neck recipe that would be very beautiful and functional. My point was just to offer you an idea to consider -which means you might like or not like it. Again, only you can say.
If it were me, I'd lose one of the Ebony laminates, and put that money towards a set of bass & treble controls. My understanding is that it's $400 retail extra for ONE set of toggles and $500 extra for ONE set of knobs. So you could switch the center lam to Vermillion and get a set of bass & treble controls for about the same amount as your plan, which would give you a lighter bass, with the significant added flexibility of the bass & treble controls and a more colorful neck with virtually the same amount of Ebony oomph as with 3 laminates; my understanding is that 2 would be virtually the same as three. This is what I would do.
But you are not me, and, as others have said, you should get YOUR dream, and what's right for you -which is not necessarily what is right for me. Only you can say. And don't take my word for it, discuss these points with the experts, Susan and Mica if you have concerns, and/or want clarification/verification of these points.
Don't let me or anyone else scare you out of what you want. Get what is right for you. The purpose of my post was to respond to your ideas, and to give you food for thought. I thought it was worth mentioning that you might consider the bass & treble controls, and that you might consider switching one of your Ebony lams to Vermillion to spice up the color, lighten up the bass, and use the money saved to add the additional flexibility of bass & treble controls for about the same amount of money.
If this sounds appealing to YOU, then you might consider or do it; but it's not like there's anything wrong with your plan. More than 99% percent of the Series basses out there DON'T have bass & treble controls... and I've never heard a Series owner complain about the lack of e.q. controls. But there's a simple solution if you want a Series bass that ALSO has these controls... order it!
I look forward to seeing your bass in FTC. It's going to be REALLY awesome -with or without bass & treble controls and/or Vermillion in place of a 3rd Ebony laminate!