As far as the ride height adjustment goes, you can use the "clean threads" dimension as a reference point. Make that adjustment "no load". As for the strut rods, get them positioned "generally", but NOT with final torque. Snug might be a good orientation as they WILL move from "no load" to "ride height". Some dielectric silicone can be a good lube (as you'd use on the plug wire boots). Same with the lower shock absorber mounts, snug.
As you ease the jack down, things will settle and move until you get to ride height.
The service manual mentions some control arm to sub-frame measurements. Many use the wheel opening molding. If both the lower control arm bumpers are in good shape and even in height one side to the other, you can use the dimension (open space) between the bumper and where it contacts the sub-frame in full compression, by my own observations. As for measurements? You can eyeball the car and make sure the rocker panel is parallel with a flat road surface. Extending the "line" of the lower rocker panel through the wheel cover, the line should "hit" the same part of the center of the wheel cover.
Doing the "snug", then tighten at "ride height" ensures all of the rubber items are basically centered in their range of travel. This means they flex equally in each direction. As mentioned, if you tighten them with the suspension at full extension, when you put the car on the ground it will preload the bushings, when they weren't designed for a constant preload, their service life will be compromised and shortened. SAME with the lower control arm pivot stud/nut, too! Final torque at ride height.
Recheck the ride height in a few thousand miles or so as the rubber in the lower control arm pivot will settle-in, too. When you get some more miles on it, then a normal wheel alignment can be done, for good measure.
In theory, if you didn't touch any of the camber/caster adjustments on the upper control arms, things should be good. Probably similar with the toe-in adj.
CBODY67