Very solid info so far. Just to chime in a few cents-worth...
Am I reading it right, that you train 5 or 6 days a week, you just don't have specific days set - like Mon is workout 1, Wed is 2, Thurs is 3, Fri is 1, etc.?
If I'm following that right, then I think you'd definitely benefit from getting on a more structured, pre-designed program. Deadlifting 3 or 4 times per week and squatting 3 or 4 days a week will eventually wear you down, unless you're totally on-point managing the volume and intensity. And if your nutrition is off-track even a little, expect an issue sooner rather than later.
Ben Bruno had a great 4 day a week template specifically for college students. Take a look:
I also think you're taking "focus on the big lifts" a little too literally. When you're doing full body workouts multiple times per week (like you're doing), you can definitely benefit from a little more variety while sticking to basic, general principles. Consider changing the sets/reps or the exercises each session (like you're kinda-sorta doing already).
Also, silly little question, but what's your particular goal? That's going to have a say in the "best" way to progress the weight, sets, reps, or whatever.