Do ya have any pics of what you are trying to do? If you have the truck up on a jack maybe the bolt isn't long enough to get lined up. I just did my truck I used the Biliesten shocks. I had to move around the bottom flanges to get it to line up correct. I took off the tires for the fronts only, and put it on jack stands, and everything worked just fine.
Maybe some one with the KYB shocks will chime in, there are people on here that have them I'm fairly sure of it. Good luck