Did you remove invisible cubes?
You could write a simple function to remove any cube,
that cant be visible from the outside.
Just itterate over all cubes, and mark those invisible, wich have
a solid cube on all 6 sides.
This cuts down the number ob cubes by 80% on average.
(you probably want to do this before exporting the data to wmb)

Also check that the cubes are exactly on non floatingpoint positions, this should help the
buildprocess a lot.