Knees in on squats usually points to glutes being weak and/or inactive in the squat. If you are squatting wide-stance, add 'push the floor apart' to your list of cues. Also, do some glute work for assistance.
Elbows out on bench points to setup first (most lifters can add weight to their bench instantly by adjusting their setup for their specific leverages). Get your setup and form nailed down FIRST. Then, I'd take a look at shoulder strength. You're likely flaring the elbows because the pecs are taking over for the delts. Heavy triceps work will always improve your bench, but most don't know how to do it right for bench assistance. Heavy front-delt work will help tremendously, as well.
As for 3 + 4? Meh. Hard work + lots of good food trumps magic program. I've seen guys with "horrible programming" make great gains just by eating and going all-out every time they hit the gym.