Well, here I go with that same advice.
Don't spend so much time thinking, planning and calculating. Spend more time experimenting and learning by making mistakes. Assembling a large and diverse collection of methods and techniques will lead to confusion. Give a method a try - go for it and see what happens. Take a saddle out, cut it lower, make a new higher saddle. Rinse, repeat, etc. That's really how we all learn!
Shims can be just fine, but thinking in terms of .001" isn't appropriate for adjusting saddle action. The smallest measurement I use for that would be 1/64" and that's cutting things much closer than I need most of the time. Usually my adjustments are in increments of 1/32". Unless there's a compelling reason, I don't shim saddles to raise them any more than 1/32" for structural reasons. I make new saddles to go higher. But, after decades of doing this stuff, I have a quick routine for making saddles. Earlier on, I did more shimming.
I do raise nuts by shimming sometimes and there I do work with finer measurements. But, the fact is I NEVER NEVER NEVER measure how much higher to raise the saddle. I simply stick shims under, string up, and check nut action. My favorite shims are sticky labels and they are dead easy to make and use - read this:
http://www.frets.com/FretsPages/Luth...m/nutshim.html
Yeah, yeah, there are all kins of ways to get the job done, and all kinds of arguments to be made about tone, but until you master the simple stuff, don't waste your time trying to be perfect right out of the gate.
In the words of Bob Taylor, "Michael Jordan didn't get good at shooting baskets by standing and aiming for hours on end. He shot and missed, shot and missed, until he learned. You don't get good at making guitars by planning and reading - you get good at it by DOING it over and over."