Bear with me for a second here. The way JBA says to install the spacer is ABOVE the knuckle, thus moving the knuckle down half an inch. If you install the spacer BELOW the knuckle, that would effectively just move the nut down enough to use the nut appropriately for the cotter pin hole.
Take a look at my (crudely drawn) picture. The way I see it, the spacer moves the knuckle down just a bit if the spacer is between the ball joint boot and the knuckle. Is that not correct?
For reference, center picture is Bob's OLD setup. Same ball joint, no spacer. Left is his new setup. Unless it's a new ball joint with a different stud length? But then that length would need to be exactly .5" longer.