Andrew,
The only one I can answer for sure is #1 - the bass and treble pickups are the same and interchangeable.
By upside-down you mean spun horizontally, right? As in the Alembic name towards the fingerboard? I've never tried that but I wouldn't think you'd be able to hear the difference because you'd only be a one half turn of wire off normal. Interesting question though. Of course if you flipped the pickup over so the bottom faced the strings it would be out of phase and things would get weird.
The new vs old pickups should also be very similar. I believe the newer ones have a more accurate count of coils and so are more "matchable" than the older ones, but the sound should be the same.
Jimmy J