Aha, glad to hear you have had some communication with the mothership already. Stand by and you'll get it sorted.
In the meantime let me suggest something... I'm a bit of a wire-head myself so what I would probably do is remove that transformer (in anticipation of replacing it anyway) get it on the bench and see if I could test the windings with my volt-ohm meter to determine what's going on.
You've learned that the transformer in place is in fact the multi-voltage model and you can see that for your 100V Japanese setup the primary side is using the Black wire and the White wire. The Green and the Orange wires are insulated, bundled up and unused. Those are likely the alternate voltage inputs.
I found a picture here:
https://www.talkbass.com/threads/alembic-f-2b-preamp.1294425/Of the inside of a more recent build presumably wired for US power. It looks like in this case the Black and Green (wound together) are being used for the primary while the White and Orange are unused.
Then the picture in this thread:
http://www.alembic.com/club/messages/449/8044.htmlof an F2B which is conveniently wired for 240V. And although harder to see it looks to me like the White and Green wires (twisted together) are unused and the Black and Orange wires are what are being used as the primary.
So my interpretation of all this is that Black is one end of the primary winding, White is the 100V tap, Green the 120V tap, and Orange the 240v end of the winding. There's a chance that once removed you will see markings on the top of the transformer describing the connections but I'm not sure because this may be a custom made component.
You'd of course want to confirm all this before applying any power (!!) but in the meantime you could certainly check for continuity between the Black and Orange wires. For the secondary you'd need to unsolder at least one of each of the pairs so you can check the transformer without any other circuitry in play. But again, I think you should find continuity between both twisted pairs.
What you DON'T want to find is continuity between the primary winding and any of the secondary wires. Plus the two secondary pairs should be isolated from each other so nothing between the Red or Blue sides.
Anyway, excuse the long story. And take this all with with a grain of salt because I am only an amateur electronics dabbler. I don't think I've ever done this kind of test so I don't even know what kind of meter readings to expect, but I understand what should and shouldn't be connected.
You'll get that thing up and running soon. We're all happy to see somebody giving it some love!
Jimmy J