You don't have waste at 4 1/2". You cut your fabric into lengths that are longer than the repeat, some length that is a multiple of the repeat but is easy enough for you to handle and stack. For example, with a 12 inch repeat you might cut your fabric into lengths of 36", always cutting on the same spot in the repeat. With your 11.5" repeat, you could cut 34.5" lengths. Then you will be able to get about 7 squares across the fabric, using up 31.5" of the 34.5" width.
You may also want to cut your fabric down the center, parallel to the WOF, so you don't have such a big piece to manage at once. If you do that, you will have a measurement in the other direction of about 20", which will get you 4 squares. This isn't a waste of fabric, since the full 40" would only give 8 squares.
Altogether, if you're working with fabric that has been cut 20" x 31.5", you will get 7x4=28 squares (4.5" each) out of each stack. Out of about 4 yards of fabric (a little less) you will get 56 squares.