The differences between S1 and S2 electronics are:
1. S1 has a 3 position Q switch for each pick up with one no-boost and two separate boost points at different frequencies. S2 has continuously variable Q switches (allowing you to pan a range of boost frequencies for each pickup).
2. S2 has a master volume pot and S1 does not.
Apart from these differences, the difference between an upgraded Signature Deluxe model (to S1 or S2 electr.) and an S1 or S2 model is in other standard features. Some include:
S1 comes with chrome plating, surface mounted logo with shell. S2 comes with inlaid logo, Continuous wood back plates, gold-plated hardware and side LEDs. Both S1 and S2 have purpleheart neck lams as standard (Signature Deluxe does too). I can't find an Alembic-pages references to this, but James says the S2 comes standard with a 7 layer laminated body, while a Signature would have only 5. His MK Deluxe w/ S2 electronics is at
http://club.alembic.com/Images/411/460.html?1054003279.
Here's the real kicker: S1 and S2 models come with only the standard body woods - Coco Bolo and (I think) Flame Superb Walnut are upgrades (Youch! $1,600 for Coco front and back). On the Signature Deluxe the upgraded woods are standard.
That's why I have ordered a MK Deluxe with S2 electronics and the body and other options I was looking for. Big savings. Some of the standard features from the S1/S2 are appealing, but I found the ability to pick and choose on an a la carte basis, AND to get the wood upgrade for nothing in the Signature Deluxe presented me with an offer I could't refuse.
Bill