@ CT - Would it be ok to substitute the Power Clean Day with something like your Structural Lats workout? Because I dont think Im too proficient with the olympic lifts.
And if im using the Box Squat as a main movement what assistant exercises would be best? or should I still treat the weaknesses like a Back Squat in terms of assistant exercises?
No. If you don't do the power clean, do a second deadlift day that is lighter (same scheme as the lighter bench/squat day). After your lighter deadlift work (normally something like 80% 5 x 2) you can do 2-3 lats/back exercises.
It depends on what your weak muscles are as well as the depth of the box you are using. A good assistance exercise for box squatting is ... drumroll... lower box squatting (squatting down to a box slightly lower than the one you are using a your main movement)... since true box squatting (a la Westside, NOT merely squatting down onto a box) is posterior chain dominant so other assistance exercises can be barbell hip thrusts, arched back goodmorning or Romanian deadlifts... for the "overload" assistance work you can do box squats from a higher box.
OK Thanks for the help. Ive started the program and will let you know how it goes.