Frequency, intensity, volume, fatigue, recovery, etc are all factors that can be manipulated to create an effective program.
That's one way to pull off an upper/lower program. The options here are almost unlimited in how to set it up but I'd caution over exercise selection. Keep the main lifts barbell compound lifts (you can use dumbells and dumbells will actually be superior to barbells BUT only up to a point, when that point is crossed you'd have revert back to barbells). You laid it out correctly but putting big compound lifts first: squats, deads, bench, incline press (although I'd pick bench OR incline and the other use overhead press, I could go into my reasoning if you wish but it's usually better to use an overhead press and a bench or bench variant not 2 bench variants unless you're aiming for a specific goal or addressing a very specific weakness). The exercises that follow immediately after usually should be tailored to your specific weaknesses in each of the primary compounds. do you have a sticking point at the bottom of your bench? Add in illegal wide grip bench, dead bench, paused bench, dumbell bench, cambered bar bench, strengthen up the shoulders, chest and lats. If you get stuck at the midpoint choose an exercise that strengthens chest and delts. If you have trouble locking out choose an exercise to strengthen your triceps (CG bench, dips, 3-4+ board presses). Theses first few exercises should always be free weights barbells or dumbells. Not only are they able to be loaded higher but the involve many more muscles than machines. Some muscles will get direct work like the erectors/glutes/hams/low back in dead lifts while others are indirect or isometric like lats and traps (work to keep the bar horizontal to the ground and close to the body, if you have trouble keeping bar close to the body, your traps and lats need strengthening). Understand most muscle groups are agonists in one lift and have antagonists while in another the role can switch. In deads the erctors are agonists (primary movers) and the abdominals are the antagonists but in a squat the roles are reversed. FREE WEIGHTS WORK THESE MUSCLES AS A WHOLE SYSTEM. <----that's the key to this, working your body as a system not a series of isolated muscles. That's why the primary and secondary exercises should all be free weights. The last exercises can be machine or cable if you wish since the final exercises could be thought of as burnout sets, volume sets, back off sets etc. 95% of the work necessary for progress has been done by this point so final exercises are greatly reduced in intensity and the compensation is the volume. The primary movements should be around the 3-5 set range and to keep intensity high you want 8 reps or less (5is a great balance point) you can choose to do less sets of very heavy singles, doubles, or triples - moderate sets of 5 reps - or more sets of 8ish reps. Secondary exercises should be scaled back on intensity and volume somewhat so overtraining wont happen (over reaching is fine BUT NOT overtraining) maybe 2-4sets of 6-12reps and the final exercises should be higher volume but very low intensity (think almost lactic acid training) 4-5 sets
8-10+ reps they should be performed quickly and easily with less rest in between sets.
Now you can do upper/lower, push/pull, upper/lower AND push/pull, hou can do heavy and light days, max effort and dynamic days, the list goes on and on. It should be tailored to your goals and something that interests you to keep your motivation up. Sorry for the jumbled mess here but it's so in depth and there's a million tangents to go off that I just wrote it as ideas popped into my head instead of putting it down from beginning to end with flow lol.
I haven't hit a plateau yet with my 5 day split, but I am always interested in this type of methodology which I've been reading about in the book you suggested. 
Great post as always Doc. 
