Hey Mike,
I know a few people on nano-reef have drilled their biocube's and it is 50/50 on whether it will break or not. So, drilling two holes, your chances don't look good

What are the dimensions of the last chamber? I picked up one of those new Maxi Jet 1100 @ 294gph to run my whole tank (including chiller). Dimensions of that pump are 2 3/4 IN. X 1 3/4 IN. X 3 IN.

HTH