I like option #2 better, although I'd tinker with it a bit so that you could hit everything in the three days.
Day 1) Hip dominant, single-leg, calves, core (lateral flexion), vertical pull, rotator cuff prehab
Day 2) Upper body (horizontal push/pull), glute prehab, core (trunk flexion and hip flexion)
Day 3) Quad dominant, single-leg, calves, core (rotation), vertical push, rotator cuff prehab.
Try shuffling things up week-to-week. Maybe hit your squats heavy the first week and then go with more reps the following week.
Also, regarding the four-week phases, I've actually found more success in terms of strength gains when there is a subtle reduction in the second week of programming (i.e. high, medium, very high, low) rather than just continuous building, which seems to be more valuable for bodybuilding purposes.