Going by clicks is more accurate than measuring stem protrusion. Use your fingers to feel the first few clicks, when you can't the nuts farther with your fingers use a mini needle nose pliers to give them a few more clicks.
If you get a long/wide flat head screw driver, you can make a good notch in it so it will engage the retainer nut. You can go through the top to make quick adjustments after its together, much faster than going through the side. Actual install, going through the side is the only reasonable option.