First of all, stop that program immediately. It is absolutely thoughtless and is not intended to build strength. College football lifting programs arent worth the paper they are printed on.
Don't switch routines up so much. 5/3/1 for football is awesome. Buy that book and the original 5/3/1 book, read them both until you have a pretty good understanding of the program and why you are doing the things you are doing, and then lift your ass off for a year before you change the program.
Youre still young. You could literally walk into a weightroom and fart on a dumbbell and get stronger. The only reason you would not be getting stronger is because your training is not consistent or you are not eating enough.
The one legged squats seemed like some sort of warm-up and the idea behind them is that you activate stabilizers in your hips that dont get activated during normal squats because the lower back and abs are the limiting factors in how much weight you can actually squat. This is the kind of stuff funtional training enthusiasts have wet dreams about. The problem is, if the lower back and abs are weak and failing first, why in the fuck would you completely take them out of the equation? Also, the stabilizers arent getting enough work in regular squats because all of the assholes that do research on this kind of stuff only use submaximal weights. Maxmimal weights elicit recruitment of what Stiff called "survival muscles" that only get activated during two points in life:
Lifting max weights
During fight or flight
If you really think about it, those two time periods are really the same thing.
Anyway, doing 6-10 exercises like the ones shown in the workout don't make you stronger. Which is why football players are the weakest athletes on the planet.
I would kind of think ping pong players are weaker.....
College programs are bad though. The program at my highschool was terrible. One of my friends has a full ride for football, and he got weaker when he went to a D1 school. He was pretty strong from a shitty program, like a 375 clean... he recently told me his clean is down to like 325, and his squat is only like 365. Bench is like 300. They don't do deadlifts heavy enough to know a max. His vertical is also down from like 39 to 37. Pretty sad that someone that is that bad at building strength is training kids at a division one school and making them weaker.
The only thing that he says has improved is his specific skills, and his sprint speed.
I also bet his occurance of injuries went up too. If the CSCS exam was one fill in the blank question: "blank" and conditioning coach, 99% of the people that take it would fail it.
I have heard that example you gave about 50 million times. Its sad really. The NFL is even worse. I have a copy of the Texans offseason "strength" manual... its 90 pages and there is only 2 pages about lifting. Sessions are described as "Do leg exercises for sets of 12, arm exercises for sets of 8, and core everyday." I wonder why the Texans suck... except for Brian Cushing.