Totally agree, "jouncing" the car to settle the suspension doesn't work effectively. The camber and toe changes with travel, when you jack the car up and lower it the tires make contact with the ground with the suspension fully extended. Then the friction from the contact patch of the tires tends to resist the changes in suspension geometry as the car is lowered, effectively holding the suspension up. It requires rolling the tire to fully settle the suspension.
The only way that doesn't happen is if the tires can slide easily on the ground, so narrower tires have less of this effect, and wider tires worsen this effect. Putting the car on slip plates (like when it's being aligned) solves the issue.
I really doubt that loosening the re-torquing the suspension at this point will make much of a difference. If you have rubber LCA bushings, and they were torqued with the suspension fully extended, it's likely that your LCA bushings have given up by now. If they're still in good shape then they were probably torqued at ride height, and the car may have been lowered (or settled further with the original torsion bars) after that. So raising it may have put them closer to where they were torqued. Either way loosening the LCA pivot nuts and re-torquing them won't hurt anything, but in your case I doubt it will change much either.
There is definitely a procedure for setting the length on the adjustable strut rods, I'll add it below RRR's quote.
Mostly agree, it's best I think to do this with the torsion bars installed and only the torsion bar adjusters removed. The more suspension that is assembled the closer the results will be to what's happening when it's going down the road.
I set the LCA up to start so that it is perpendicular to the frame, and the goal of the adjustment is for the LCA to be free of any binding when it travels up and down. Adjustable strut rods are not for adjusting the alignment specs, although you may see a change in the alignment numbers after installing them. The goal is the free movement of the LCA up and down, while reducing movement fore/aft.
You'll want to have as much of the suspension installed as possible while still being able to check for resistance/binding. So, torsion bars in, UCA's, spindles, LCA's installed. You'll need to remove the torsion bar adjusters so you can cycle the LCA up and down by hand. You'll also need the shocks out, and if you have a front sway bar you will want that disconnected as well. Then cycle the suspension up and down, from bump stop to bump stop, and check for binding. If you know where in the range of travel your ride height is that will be better too, since you'll want that to be the neutral spot. It takes a little trial and error, especially the first time, to get a feel for what is normal resistance and what is binding. When you think you have it good, put another turn on the adjustment in one direction or the other and see what that does. If you're right, it should be more binding, if you're not, you may get less so that's the direction to keep adjusting until the binding starts to come back.
I've found with my cars that the adjustable strut rod ends up being a bit shorter than the factory strut rod, but I also use Delrin or poly LCA bushings, so the LCA may be slightly farther forward with that arrangement than with the stock bushings. Typically I've found that the ride height/neutral spot has a small amount of tension on the strut rod when the LCA is most free from any binding within its range of travel. This also keeps the LCA from moving backward any while it's traveling, which is good because that movement results in a negative caster change. This may be different for some though because your ride height may not be centered between the bump stops.
Not really. The only way it won't change your alignment is if your strut rods are already the correct length. Any significant adjustment of the length of the strut rods will change your alignment numbers, primarily your caster setting. Changes in ride height affect everything.