As far as I am concerned, there is no definite scientific method to this. Just trial and error. Perhaps someone will come along and *****-slap me, but here is what I do:
FJR on centerstand about 20' from garage door. Make sure the lights are on low beam, as you will see there is a most excellent sharp cut-off at the top of the light pattern. High beam pattern is fuzzy and vague and will make things much harder. Don't ask me how I know this.
Now place a bathtowel over one of the lights (draping it over windscreen). Now place a piece of tape about 2' long on your garage door along the light pattern cut-offI mentioned above, and approximately centering it. Repeat for the other side. Now, immediately, you can tell if both lights match each other.
Once again, having the towel over one of the lights, I start adjusting the other one. I usually move the pattern a couple inches. I then swithch to the other light and match the same beam level.
Now its time to go riding and test your adjustments. Best results will be a long straight two-lane road with no other ambient lighting around. I find that by stabbing the front brake quickly and gently, I can induce a quick dive which will give me a feel for where the top of the light pattern is. Once again, it is imperative that you do this on low beam! Though, you can also do this on high beam too, to get an idea where the center of intensity of the light pattern is.
You may have to re-adjust a couple times, but I have found the above method very useful.
The only problem will be loading. Once I had my lights adjusted for my normal local riding, sans bags, I found that when loaded for long distance trips, with bags on and loaded, fuel cell full, and luggage strapped to it, my headlights were once again pointed too high. And yes, I did increase the pre-load.
I am not one for adding unnecessary bling to the fjr, but an electric headlight adjuster would be very applicable and convienant IMHO.
Good luck!