In Charles’ original article, he outlined arm programs for each of the four phases. I haven’t tried this program yet, but I think it would work very well in an arm specialization program. If that’s what you’re looking for, bringing your arms up to par, try the following split:
Tu: Hamstrings, bent knee calves, traps
Th: Chest, Back, Shoulders (balance the pushing and pulling)
F: Quads, straight leg calves
I would personally recommend keeping the volume of each workout to about 14 sets, which is slightly lower than what Charles recommended for most of the phases. As an example, in the first phase of 5 X 5, use the first exercises for 5 X 5, then the second two superset exercises for only 2 sets of slightly higher reps, maybe 8-10. On the leg days, you can use the core leg lifts, ie squat and deadlift, for his 5 X 5, then an assitor exercise for 3 sets. The remaining 6 sets you can use for the calf and trap work.
Oh yeah, back to you're original question. Superset the A1/A2 exercises. With maximal weights, that means do a set of A1, rest a full 2 minutes, then do a set of A2. That will give you almost 5 minutes rest between sets of the same exercise.
Hope this helps.