So I had an e-mail this week referencing Wendler's article about full body training, and how one would implement the pre-hab work I wrote about into that kind of template.
This is not a difficult thing to do actually.
If you look at MadCow's old template you can see after the big 3 movements are done there are some other things scheduled to be done. I actually found the work Glen laid out afterwards to be rewarding and productive. So why couldn't pre-hab work just fit right in there instead?
Squat - light
Deadlift - heavy
Bench - light
Since this is a deadlift day, an easy solution is just to throw in some leg and bicep curls.
Barbell Curls - 3 sets
Leg Curls - 3 sets
Squat - light or medium
Bench - heavy
Barbell Row - heavy
Since this is bench day, let's go ahead and work those pesky rotator cuffs and rear delts.
Front Raises - 3 sets
Rear Raises - 3 sets
External Rotation - 3 sets
Squat - heavy
Overhead Press - heavy
Chin/Barbell Row - heavy
Squat heavy day, so let's avoid those shitty adductor and quad strains that happen sometimes when squatting.
Leg Adductor Machine - 3 sets
Leg Extension - 3 sets
This pretty much covers everything from head to toe. If your injury history dictates that you need to concentrate on something different than what I have outlined here, then do that. But this list is pretty good and will cover the most common injuries.
Remember that consistency is the biggest factor in making sustained progress, and you can't be consistent if you are always injured.