Hey there, Paul.
Just got home from a nice dinner with my sweetie and our friend, and then I was doing a little research on the site to try and help you.
I'm going to roll through some things semi-randomly -without worrying too much about the order, or having great form.
First of all, you're set on the Series II. That comes standard with 8 controls -as I mentioned above. Plus you want 2 dimmers for the LEDs. Let's start there.
LED DIMMER THOUGHTS:
By all accounts, a variable dimmer is a must-have (or should-have) for the front Laser LEDs... they're so bright... you just REALLY want to have this control. On the other hand, it might not be as important with the side LEDs -they're not as bright. Also, you say that you want a dimmer... but have you considered how the (side) LEDs will be set up? By this, I mean... my understanding is that, as a rule, they're set up to ALWAYS BE ON on a Series bass -when the external power supply is plugged in. I could be wrong about this, so CONFIRM this. But (if I'm right) you have to ASK to have an off/on switch. Also, I'm pretty sure that (in general) the LEDs WILL NOT work WITHOUT the 5-pin/external power supply UNLESS YOU SPECIFICALLY ASK THEM TO MAKE AN EXTRA BATTERY CAVITY. My Custom Europa takes 4 9-volts -for the side LEDs. This probably doesn't matter to you... but maybe it does. IF you want to have the option to turn (either the front and/or side) LEDs off/on and/or be able to turn them on WITHOUT the external power supple (for example, with a wireless system, for gigs) you might want to inquire -NOT ASSUME- and make sure you'll get the setup you want. If you want to have an on/off switch -ask/make sure you get one. If you want to be able to use the LEDs without the power supply, ask/make sure. Anyway, you might, for example, want a variable dimmer for the front, but have the sides be on all the time (only with the power supply plugged in) and have a 3-position toggle offer 3 settings for the SIDE LEDs. I don't require any dimming for side LEDs. But of course, you're not me. But if/since you're concerned about knobs and space, a 3-position toggle might be enough for you -for the side LEDs. (And only you can say.) A 3-position toggle could let you choose between, say LEDs off/on(1/2 power)/on(full power). Or again, you could consider eliminating the side dimmer.
So this is something for you to figure out. Do you want them to automatically come on (only) when the power supply is plugged in? Do you want the option of having the (front and/or side) LEDs work WITHOUT the power supply? Do you want an off/on switch for the side LEDs? Do you want/need a dimmer for the side, and if so, do you want/need a knob, or will a 3-position toggle do? If they were set up to always be on, you could have 3 levels of brightness with a 3-position toggle; or you could have a 3-position toggle that offers you 2 settings and an off position. Only you can answer these questions... but Alembic can do it any of these ways. I recall seeing at least one Series owner lamenting that he couldn't use his LEDs when playing wireless (which can't be done without the external power supply). So if this is a concern, you may want them to route a cavity to install 9 volts for the LEDs. I don't even know if they can do this for the Laser LEDs... it might not be an option for them... they might eat too much power. I just don't know -so IF this important -find out from someone who DOES know.
Another thing that MIGHT be a possiblity would be to see if they could have an innovation that does two functions at once. For example, see if they could make you a master volume with a center detent (like the pan controls) that works as a volume control with (say, for example side) LEDs on one way, and off the other way. This should be possible... but whether it would be an easy quick rig up, or an long, expensive custom job... you'd have to check with Mica or Ron.
THOUGHT ON LOTS OF KNOBS:
Again, the standard Series II setup has 8 controls, basically all knobs. And you're going to add at least one more knob for the Laser LED dimmer, and probably another knob (or toggle) for the side LED dimmer. So that's 10 controls. On the other hand, you may eliminate 2 of those knobs if you elect to go for a master volume/pan setup -instead of the 3 volume & pickup selector setup -which would put you back to the status quo of 8 controls. Or you could consider really going nuts and ADDING another knob -a balance control- and a toggle switch to choose between the 3 volume system and a volume/pan setup. I don't think they've done this before, and it would be a custom setup, and likely expensive. You probably aren't even interested, and would probably prefer to do an either/or... choose either the standard Series setup OR the simplified master volume/pan setup seen in the two examples I referred you to above, and the one Steve linked you to. But if I'm wrong and it does interest you (which doesn't sound like the case, especially as it would mean more knobs!) then you could ask.
But I will tell you that there is no need to be afraid of lots of knobs and controls. It can be done, and it can work well. It's all about space efficiency, and layout.
If you want bass and treble controls, you should get them. There are LOTs of different options and ways to address this need, and you can find a way to balance getting these controls with your concerns. If you want bass & treble controls, remember that you can choose knobs -which take up more space (and/but are more versatile) or toggles (which are less versatile but take up less space). And you can choose to have individual controls for each pickup (twice as many controls) or you could just have one set of master bass & treble controls. You could also mix & match. For example, in my opinion, a variable bass control (knob) is much more important/useful on an Alembic than a variable treble control. This is because if you DON'T have one, the only way to boost the bass is by turning the filter all the way down -which means you filter out all the frequencies above that point. A variable treble control is less important, as it's easier to adjust those frequencies with the filter & Q.
I'd recommend getting at least one MASTER SET of 3-position bass & treble quick change boost/flat/cut toggles. These two little switches take up VERY LITTLE space. Better yet, get a set for each pickup... they still wouldn't take up much space. Another idea would be to have ONE (master) treble toggle and ONE (master) bass KNOB. Again, that wouldn't take up much space. Finally, you might consider 2 treble toggles (one for each pickup) and 2 bass KNOBS (one for each pickup). But that's getting knobby. I don't think treble knobs are something that you should pursue, based on your concerns.
So you could think about this. Probably the best thing for you would be one of three things: (1) have just one (master) set of bass & treble toggles... this takes up VERY LITTLE space, and is nothing to worry about, trust me. (2) You could get 2 sets, one for each pickup. (3) you could get ONE treble toggle and ONE bass KNOB. This would only add a little space.
You should think about this, study some layouts of other custom Alembics with lots of controls, and maybe play around with drawing some layouts for yourself. You can use pennies and dimes on an index card, and move 'em around to make mockups for different configurations.
My Europa has SIXTEEN controls... and it's incredibly intuitive and easy to use. I NEVER have any problems, and can get any sound variations I want quickly, consistently, and easily. But I had them design it in a very logical and space-efficient way.
I'm going to give you some links and references to other Alembics on the site that you may or may not have seen -to study and have at your disposal for reference purposes. I'm new at doing links, so some I'll have to describe/tell you how to get to. And I may have to submit some as separate posts. I'll get started now.
First, here's Understated Elegance -from the Custom Archives. It's another Series Bass with a master volume, pan/balance, and INDIVIDUAL bass & treble KNOBS for each pickup -laid out in a very simple and elegant manner:
http://www.alembic.com/info/JEfretless.html Next, check out the Big Bass, which also has INDIVIDUAL bass & treble KNOBS for each pickup (and which also is a Series Bass:
http://www.alembic.com/info/fc_yahya.html Finally, I'll try and post a close-up of my bass and it's control layout:
You can see I've got 8 knobs, basically as knobby as a standard Series II setup... AND I've also got 8 toggles switches, 4 pairs set between the knobs... they don't get in the way at all.
You could easily do something like this -ESPECIALLY if you elect to elimate the 3 volume/pickup selector setup. Imagine something similar for your setup, like my bass above, but with only single toggles in-between the knobs.
Imagine the top row being a master knob in the center, filter knobs on either side, with individual 3-position boost/flat/cut treble toggles in-between; middle row, 2 CVQs; lower row, pan/balance knob in the middle, side and front off-to-maximum dimmer knobs on either side, and individual 3-position boost/flat/cut bass toggles in-between. 12 controls total: 8 knobs, 4 toggles, simple, symettrical, space-efficient, and giving you extra-awesome control.
Of course, this suggested layout is just one of many; it's just to offer a simple, conservative, and mininalistic -yet extra flexible arrangement.
One final example to look at:
http://alembic.com/club/messages/631/2936.html?1066333385 If this link doesn't work, do it the hard way by going to Factory To Customer, scroll to the bottom and click on Archive through Dec 31st 2003, and look for For Harrison. Another awesome Alembic with LOTS of controls -individual bass & treble KNOBS for each pickup.
Oh yeah, another really cool one on the main FTC page -about 1/2way down- is Rory's custom bass (or maybe it's Rory's custom 6-String bass?... it has LOT's of controls... and note that it's a BALANCE K with INDIVIDUAL bass and treble controls for EACH PICKUP IN ADDITION to having the standard EIGHT CONTROLS of ANNIVERSARY ELECTRONICS!!!
So it can be done!!! You need have no fear of lot's of knobs!!! If you want bass & treble controls... GET 'EM!!! If you want to go all the way, you can get knobs for each pickup!!! Just look and see... it has been done! And obviously, doing something more conservative like having just a single set of master toggles or knobs or having two sets of toggles would be no problem -even on the small Balance K body. Rory's awesome custom is proof. (And you should check it out, 'cause it's just an absolutely stunning Balance K -one of the nicest I've EVER seen. It was the one that pushed me over the edge into getting the Balance K body!!!)
Take care, Paul, hope this helps!!! I'm REALLY looking forward to seeing your masterpiece when it gets going! You're neck is already an instant classic, and one of the coolest I've EVER seen!!!
Mark