Hey Roger, glad to hear from you. I just saw your further in your profile, and it sure looks sweet. As usual, I am lurking in the shadows of the Alembic site...
I think that the conclusion that I eventually reached was that active electronics and fancy fuzz pedals are bitter enemies, and do not want to cooperate with one another. Other effects I tried worked fine, but any germanium fuzz was quickly repelled, and no amount of trim pot adjusting would solve the issue. They were mainly zvex effects I was using, but the above comments about the Rat and Fuzzface come as no surprise. Those sorts of pedals seem to be more sensitive to the guitar circuit than many other effects. For instance, a zvex fuzz factory can do a pretty good theremin impression, and at the right settings, you can even change the pitch with your volume and tone knobs. With active electronics everything just sounded liefless, lacking most of the high end definition.
I wonder, would alembic ever consider building a guitar with an active/passive switch, or do the nature of their pickups preclude this as an option? Forgive my ignorance regarding electronics.