If you haven't had step rails on in a while (or at all), the bolt holes will get gunked up. I used to remove my step rails before I went off road, then reinstall them when I got home.
I boogered up a couple of the bolts by cross-threading them in dirt-filled holes. With the fine threads used by Nissan for the step rails, it's easy to do.
I installed my Shrocks by myself and didn't have any problems lining everything up.
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2002 Just Blue XE 4x4