godoze,
Sounds like a nice project. It's certainly difficult to decide when a custom really becomes a custom, have you discussed this with anyone at Alembic or an authorized dealer? From what you've described, it sounds like you'de be better off starting with a MK Standard as your base model, especially if you're seriously considering the signature electronics. I think a Rouge with your options will price higher, just a thought and I may be wrong.
I talked to a local dealer about a custom Alembic and they start pricing based on the electronics you wanted; I don't know if that's how Alembic starts pricing.
Being able to interchagne almost every feature can be a challenge, albeit a fun one. I'm looking forward to whatever you build, go, man go!
Mike