Did you put the weight of the truck on the springs before tightening the bolts at the bushings? If not it can bind them up to be a lot higher than should be. Don't ask how I know....
I used the Redhead box and the Borgeson U-joint link. I love them both. It drives much more precisely. The Moog ball joints however, are tight as a nun's a$$. When they wear in it will be even better.
I used 3.5 inch in the dash. I agree with kick panel speakers not being all that. I did not use a center channel, but loaded up every where else. I put 6.5 inch components in the front doors on spacers. If you have manual windows you can cut them in down at the bottom. I have power windows...