OK, you're on the right track man.
You understand that training should go in some kind of logical progression. You understand that assistance lifts build up your main lifts. You see the need to increase the weights you are lifting. You see how the micro cycles make up the blocks, which fit together to make up "Periodization." So all of that is awesome and great.
The problem is that you're not great at selecting which lifts should go on which days. Your sets/reps/percentages are also not set up in an "optimal" way.
You just need to follow a simple and effective training program for awhile. Follow the rules and make the gains. Then, use your book knowledge to understand WHY the program is working.
For Your Accumulation Phase use some kind of REP PR system. "Regular" 5/3/1 with rep PR's is great for this. Thge percentages and waves and rep ranges are all planned and proven,
"Greyskull" uses a similar "plus set" approach.
You could also use the EMOM approach C.T. is talking about in his forum right now.
Or you could try to increase the number of sets you do in the same amount of time, like dude outlines in "The Westside Method Thread."
Then, for your intensification phase, use some kind of plan where the sets and reps stay similar, but the weights go up. Include back off sets, to move lighter weights for "power." Wendler's 5's Pro is great for this.
C.T.'s 5/4/3/2/1 ramp could also work.
A Westside Intensification wave with 50-55-60% could work.
You could even just do like 6 weeks of "starting strength" or some kind of similar plan if you wanted.
These "blocks" should be made up of Two, 3 week waves each. Westside and Wendler run their programs this way, so its convenient to follow them.
Personally, I like assistance work, but its important to keep it from taking away from your progress. Push Press, Front Squat, Paused Squats and deficit deads are good lifts, but they are serious! They crush your whole body. Important "secondary lifts" like that need to be treated carefully. Westside, or Wendlers "Simplest Strength Template" will get you up to speed on how to include these lifts.
Follow the experts for 12 weeks. Check out how they implement the concepts and sciences that you've been studying.