You will definately have a noisy ride with lots of cluncks without a locknut. The JKS control arms work like that without a lock nut but they have untrafine threads, a bush on the inside and they are pumped full of grease absorb some movement and noise. I'd suggest you fit a locknut and then loosen it when you go offroad, but keep it locked on the road.
In term of the adjusting lengths. I recently installed adjustable short arms in the stock locations with a 6" lift. At first I set everything according to Yucca-Man's website which says it should be 17" for the lowers and 15.5" for the uppers. That combination gave me caster of 11 degrees with the pinion pointing downward from horisontal (I didn't have a driveshaft fitted at the time, but it would have been horrible vibrations). I liked how the lower control arms positioned the wheels nicely in the centre of the wheel wells, so I kept their lengths as they were at 17" and extended the top ones as far as I safely could. On an alignment machine afterwards this gave me a caster of 5.30 degrees and the pinion/driveshaft angle at around or just under 5 degrees. This works well in terms of handling and I have no noticable vibrations. Now, to remember what the lengths of the upper control arms were???? I'm under correction, but I think they turned out to be also set at about 17" - somehow I have the figure of 430mm stuck in my mind, I'll measure and if it is something completely different I'll post back here..
What I can say is that at 6" lift with short arms in the stock position one would ideally want drop brackets or long arms.
This what the angle look like!