I saw that you linked to my library here.
In the ShiftPWM support topic I posted a matrix version of the library, which is not up on my website yet.
If you make a layer of 100 LED's as the columns in the library and 10 rows to alternate between layers, you can use that version to drive your cube.
Milamber used it to drive 1024 LED's, see his topic as well. On a 328p, thats about the limit, due to memory restraints.