When doing box squats, do 1-2 light sets of Deep Squats

Something your missing that may help you in the future. I have preached the need to be somewhat flexible and patient. One thing that would have helped you doing box squats for so long was to allow yourself to switch them out every so often for regular squats. Keeping youself familiar with it and so on and preventing that culture shock of swithching suddenly. Also you can alway hit a set of light squats as a backoff as long as it is really a backoff and not ball's out. Higher reps.

Something I've mentioned and witch I really believe to be the case is that practising and also learning a movement for the first time is really better done with higher reps. This cements the movement patterns quicker and better and gets you greased up. At any time when you get away from the main movements you can still use this concept to keep in practice. The body doesn't just deal in intensity and volume. It deals in patterns of recuritment which I shorthand as "movement patterns" as a catch all of all the different things going on. Even if you don't feel a set is "productive" in the traditional sense of progressive overload it is still productive in other ways.

In fact I count this as one of the drawbacks of the 3x5 Rippetoe thing for absolute beginners. It's a good set range in terms of using moderate volume but not a good range in terms of learning the lifts. Plus the fact that absolute beginners will react the same to whatever you give them.

You don't have to necessarily do back off sets every time...and sometimes you can just completely replace the box squats for some appropriately heavy squats. Keep in mind that you can rely on any one method to keep you squats healthy. And also keep in mind that some "catchup" is just part of the game if you train this way but for the most part you should be able to maintain squat form and confidence while you're going along.

no situps and crunches

The hip flexors are part of it. That can be overcome by going into posterior pelvic tilt and doing abdominal vacuums...but the biggest reason is that they are bad for the shoulders and not to mention the back....(which again indirectly leads to the shoulders). And they are simply not as effective as some of the other choices. For flexion standing ab pulldowns can be much more effective. You can add more weight and you can posteriorly tilt the pelvis and do the vacuums which will effectively remove the hip flexors from the equation.

People go around and around about all this and are always trying to come up with modifications to the pushups and crunches to make them better....it's such a waste of time when there are so many other options. Do reverse crunches instead of crunches and it will be much better. You can add leg weights and doing hanging knee or leg raises is sort of a more advanced version of this. BTW, for hanging stuff I actually do more LOWERING that raising.

For instance for hanging leg raises I will bring the knees up all the way to my face then lower them down WHILE straightening the legs until my thighs are parallel and my legs are straight out in front and then I will slowly lower...and repeat. I do ALL of this while maintaing a posterior pelvic tilt (that means the top of your pelvis is tilted to the rear). There's just all sorts of shit you can do. And isometric stuff is good.

It's very important to find ways to recruit the external obilques more. So that's why the torsion exercises come it. And things like cable woodchops are good. ALL of this type of thing is going to strengthen the entire abdominal complex. You really don't need to worry about situps and crunches

I am not convinced at all that someone needs to do EXTRA internal rotation exericises

The only thing I can add is that I am not convinced at all that someone needs to do EXTRA internal rotation exericises. Like I told you before, almost all your major upper body exercises involve some aspect of the internal rotators. The internal rotators are huge muscles. Especially compared to the external rotators.

The major internal rotators are the lats, pecs, teres major and subscapularis. The first three for sure get worked in abundance and are going to tend to be dominating to the externals. What you'll find is disagreement about the subscapularis. Some will say you need an isolated internal rotation exercise to hit that muslce. It is a muscle that lies underneath the scapula hence the name. The mistake people make is that they think it is very tiny like the externals because you can't see it. But in fact it's pretty darn large. The will say it will be inhibited by the larger internal rotators and thus cause imbalance (it is an important humeral stabilizer)....so it needs to be strengthened.

The problem is this assumption doesn't seem to be indicated by research. Basically if the internal rotators are hypertonic and dominant the subscapularis will be also. I've never seen anything to indicate that the subscapularis becomes inhibited by the other internals in the general shoulder disfunction syndromes. If anything it tends to become OVERWORKED if the scapular movers and external rotators are weak because it will have to take over some of the stabilizing role...of for instance the suprispinatus.

You know I have a lot of respect for Eric Cressey but I disagree completely with his statements about working the subscapularis. Until he shows me some examples of it being inhibited which he has never proven.

So to sum it up....I would avoid "internal rotations" as a prehab excercise. That is, the actual isolated type that are supposed to target the subscapularis more. There are other prehab type exercises that may involve some internal rotation but will also hit some other small but important muscles. This is fine but just keep in mind the relationship I layed out about the abundance of internal rotation in the average program. It is also important to stretch the lats and pecs for this reason. However I am not talking about DC style stretching!