Yeah, the bushings for the cigar pen are REALLY easy to get turned around. To avoid that, I "number" my bushings.
First, I use calipers and measure the bushings and fittings. Then I line them up in the proper order, working from left to right, with the clip end on the left. I also check these against the given measurements from the kit instructions. Then, on the first bushing, I take a Sharpie and put a black mark on the end of the bushing. I put it on the end that slides into the brass tube as this will not be rubbing against any other bushing or will be effected by sanding. On the second bushing, I put two marks, and so forth.
When finished, I can turn with the pen facing in either direction; I just have to order the bushings accordingly. ALL of my bushings start with the first bushing at the clip. Consistency is key.
I have been using this system for a while, and have not had any problems.
YMMV