Last Oct. , I installed the Lorenz Bilstein 5100 Suspension System on my '03, 3500, 4X4. I just checked & the amount of threads protruding out of the top of the nut is a bit greater than the length of the nut, itself. Probably a bit more than 3/4" of thread showing out the top of the nut.
Is there any chance that you may have installed "both" bushings underneath the shock tower? That might create a situation that only gives you a few threads to install the nut on. There needs to be a bushing both underneath & on top of the shock tower before the shock is installed.
Good luck with the installation.
Joe F. (Buffalo)