The "instructions" I received with my Bloody Knuckle (same as JD) arms suggests "at least 2 threads showing behind the jam nut". They aren't great instructions, but I could email the .doc file to you. PM me an email address & I'll forward it if you like.
If your radius arm frame brackets aren't "perfectly" installed, the front end could be out of square to the truck. The alignment of the truck would be off, if the wheel base on the left side, is different from the right side wheelbase. You can adjust, the heim joints in or out, to make the wheelbases match. Its probably more important to get the sides the same, than it is to make the new wheelbase match the original wheelbase measurement. Take repeatable measurements, from left & right sides, from one point on the rear axle (maybe center of a backing plate bolt), to a point on the front axle (I used the bottom ball joint grease zirk). You don't want to measure anything on the knuckle, since it moves with the steering & changes the measurements.
I read about your alignment issue in another thread. I swapped to 79 Bronco axles when I installed the long arms, so my experience with caster will be different. I have a 14 yr old JD 3.5" lift w/6.5* bushings. With the long arms installed & bushings installed correctly, my caster read 14*. I flipped one side of the bushings, and lost about 4* caster, to about 10*. When I completely flipped my bushings (both front & rear) I'm reading about 6*-7* of caster & the truck drives great. I had expected to buy another set of bushings (maybe 2*) but found the reversed 6.5*s worked out. Its worth buying or fabing up a tool & angle finder. BC Broncos makes a tool that allows you to measure your caster with a basic angle finder. Jim Cole also said that installing the "head" (part that attaches around the axle) upside down, would loose about 8* of caster.
Chad