Triple checked all my measurements with a machinists ruler. Brass rod gently pushes up against the bottom of the air box but clears the bottom panel. On our other bike it misses the air box but brushes the bottom panel. Otherwise very happy with the performance of the damper.
I've watched several install videos and every one has a different outcome as to where the rod travels. When I installed mine I was careful to get all the measurements correct but my rod also hit the plastic. After double checking all measurements to confirm they were spot on I ended up moving the back bracket slightly up. Now the rod doesn't hit the plastic.
I wish you would have shown the adjustment. It seems that both cap bolts are fixed, but I'm not sure -Hence my previous comment. I also wonder why the end is so long. Couldn't you just cut off several inches of the rod?
The system needs the full stroke of the the stabilizer to work properly, if you cut the rod; the rod will travel inside the stabilizer body and and damage the stabilizer.