To close the loop on this topic (and the other topic I had about possible issues mixing stainless steel with pressure treated wood), I've basically completed this project.
The bookcase itself (wood, hardware, even the paint) was weighed and got about 105lbs. Recently I obtained a free grams scale (it goes for around $1200) and thought I'd be cute by weighing all the hardware. Even took an empty can of clear stain (the paint used on the wood), used that as the tare weight, and weighed a full can of paint so I knew (within reason) the weight of paint.
In any case, the 3/8" threaded rod is approximately 10" from the sides and centered front to back on each shelf. When I placed the rod through all the holes, the rod slid in and out without an issue indicating the holes were all in line.
The threaded rod goes through the ceiling, and through a 2" x 6" piece of non-PT wood that lays across several attic joists (obviously with washers/nuts on the threaded rod to hold it up). The attic joists at this point sit on the load bearing wall distributing the load downwards to the lally columns in the basement. Currently I'm letting the bookcase acclimate and settle, but, going forward, I'm laying a 4" x 4" (non-PT) wood on top of the 2" x 6" (the threaded rod will be fed through the 4 x 4) and place nuts on top. Using the 4 x 4 on top of the 2 x 6 will allow double support protection, but also reduce any wood bending (I knew a 2 x6 wasn't strong enough, and a solo 4 x 4 may bend slightly over time). Also, I'll use a bracket to hold the bookcase to the wall so the bookcase can't be pulled outwards or side-to-side. In the X and Z direction (side-to-side and outwards from the wall - if those are the X and Z axis) won't have any force on it; unless someone comes along and yanks on it.
It came out exactly as I envisioned it years back and it came out quite square. I'm uncertain how pros do this kind of work, or, even how store bought furniture is so straight.
In this case I'm dealing wit 50" length wood (11.75" wide), 1" thick. One piece was warped as a cup (on an exaggerated level) front-to-back, the width of the wood varied by 1/16", sometimes the square would be square when compared to one side of the bookcase and underneath the shelf, but wasn't square when compared to the same side, but on the top side of the shelf. This told me the shelf could be warped, or the side panel warped, or both.
Store bought furniture always seems "perfect", wood working TV shows always seem to have perfectly straight/square pieces, etc...
I began thinking, I could "rip" the wood on a table saw to straighten the sides, but then I thought: if the wood is warped, say an S shape (on an exaggerated level), when it's fed through the table saw, it's going to follow the path of the S as it rides the guard, thus giving you a smaller (less wide) piece, but still the same S shape.
If you even manage to get the S shape worked out, it can still be warped as a cup (front to back or side to side), or have a radial twist.
So I don't get how wood workers get it so "perfect". In the case of my bookcase, every shelf is leveled, the shelves are all fairly square with respect to the side panels, and some slight rocking if the side panels are pushed one at a time into the wall indicating the middle of the shelves are resting against the wall with a space on the outer sizes (this is an easy fix - I'll add a few rubber bumpers on the rear along with the bracket that will hold it against the wall).
As "perfect" as mine is, I know it's not pro and/or store bought quality, so I can't understand how pros do it.