I've installed a few MII kits. They are all just about the same. Question, are you checking these clearances with the truck jacked up, and no load on the front suspension? If so, quit worrying about it as the entire thing will settle a bunch when weighted. You have a cross member, it is likely made of 2x3, or 2x4 rectangular steel tube, likely 1/8, or 3/16 wall. You have a lower control arm, and it's wider than the cross member. There is a spacer tube welded to the cross member where the lower arm goes. There is a short spacer on the lower ball joint. Use it. The rack boot will rub the lower arm if the truck is jacked up, and by your description, you are no where near needing to worry about it. There should be a pair of washers on the lower a-arm bolt. One at the bolt head, and one at the nut. They are likely 1/16" thick each, which would take up half your gap. Tightening will close the rest. You cannot tell any thing about clearances until it's tightened up, and has loaded weight on it. The springs will look too tall, they're not. The tie rod ends will pivot upward, leaving approx 1/4-1/2" of clearance when loaded down. They say don't use lock tight. If you do, use the blue, and not the red. The major bolts use nylock nuts.

 

My lowers had 4 washers on them from the factory. They came with the bolt in them and another spacer together with the bolt washers and nut. With all four washers, one each side of the bushings, and snugged with a wrench, it seems the gap will be taken up. Nylon nuts will not loosen?

 

No, the nylock nuts will not loosen up. Some come with self locking pinch nuts too.