Another idea I just thought about would be to keep the LOWER workouts at the lower range (weeks 3-6) while letting the upper body catch up. Your lower body will be A LOT easier to continue linnear progression while letting the reps drop for upper body progression.
So an example looks like:
Week 1: UPPER - 3x12 ; LOWER - 3x8
Week 2: UPPER - 3x10 ; LOWER - 3x8
Week 3: UPPER - 3x8 ; LOWER - 4x6
Week 4: UPPER - 4x6 ; LOWER - 4x6 [Now everything's caught up]
Actually, the squatting as well as the shrugs could benefit greatly from the higher reps. After thinking about it, if you were more comfortable with an Lower body undulation, you could keep the squats in line with Upper body reps/sets, and the remainder as per above.
Week 1: 3x12
Week 2: 3x10
Week 3: 3x8
Week 4: 4x6
Week 5: 5x5
Week 6: 6x4
* Will do these reps on all lifts.
* Will repeat the cycle after you finish the 6th week.
Also remember that you could also do 2 week mesocycles per range. This IMO would be better since you could most likely progress in weights from one week to the next at the same rep/set range. This would make this program 12 weeks progression versus doing the 6 weeks, resetting back to week one, and doing another 6 weeks.