As far as changes to the program, I found doing 5x5 deadlifts to be excessive in the novice version (completely drained me) and ramp-up 1x5 DLs worked better (a la Rippetoe/SS). If you still need more DL volume for whatever reason, I've lately tacked on 5x10 on the last day after the other exercises with 30-50% 1RM weight (a la Wendler/531's Boring But Big). Also needed to add extra arm work. Calves were a lagging issue for me BUT the sheer amount of squats made them come up naturally. Otherwise, this is perfect. Stick to this protocol with adequate rest, good form and a slight caloric surplus and you'll be somewhere strong in no time.
Brandon Lilly is a beast with huge raw and geared powerlifting totals. Following his advice seems like a good idea. This calculator is for the improved Cube program described in his book 365 Strong . Lilly gives you a lot of freedom when choosing your assitance work for this program. You are responsible for your own success and tayloring the program to suit your strengths and especially your weaknesses. (If you are new to powerlifting-style workouts, check out Starting Strength . You’ll progress faster and end up back here soon enough ready to get the most out of The Cube.)