I'm not sure that tightening the stem nut (1 1/2 inch nut) to 90 lbs-ft is the right answer. I've read the links regarding this fix and have heard others state that this fix is in a MoCo service bulletin, although I've searched this site and never found any such bulletin:
http://www.harleyhog.co.uk/M_bulletins.htm
I've got an '05 Nightrain softail and occasionally have the clunk when braking hard. Its a sound you can feel as well as hear. I've read about torquing the stem nut to 90 lbs-ft and was about to do this until I started reading in the factory manual. First, the appropriate manual pages are located in three areas: The setting of the fork bearings (fall away method) is in the Maintenance section, while the front fork info and the stearing head are covered as individual topics in the chassis section. Reading all these, it appears that the bearing preload or fall-away is set first with the fork stem nut NOT torqued. Then, after all is within specs, the fork stem nut is torqued to 35 to 45 lbs ft I believe. You do not then recheck the fall away. This implies that the company has factored in the stem nut torque into the final adjustment and is important to understand. Tightening the fork stem nut WILL increase the preload on the bearings and appears to be part of the engineering. To torque to 90 lbs ft will only increase the preload and if you readjust the steering stem adjuster nut to compensate, then your fallaway will be too small and the compensation with the 90 lbs ft stem nut will not bring you to the appropriate final preload. Remember, my theory is based on the fact that the fallaway is set without the stem nut being tight, as the manual says. Then, the manual listed torque will bring it to the proper final preload. The fallaway when the stem nut is torqued is greater than the 1-2 inches required before the stem nut is torqued and this final fallaway is not listed in the shop manual.
Here is what I think is happening and how to make sure you are properly adjusting the fork stem adjusting nut. The lower yoke and fork stem are functionally one piece. It is attached to the frame through the steering head and held in place there with the fork preload adjusting nut, itself held in place with the large 1 1/2 inch fork stem nut. The other mounting points are at the pinch bolts on the forks. Here is where I believe there may be a problem. When the fork stem adjusting nut is tightened or loosened when setting the preload, the lower yoke must be free to slide up and down not only in the steering stem but over the fork tubes as well. If the lower yoke is stuck to the fork legs and doesn't move as the preload nut is adjusted, the lower yoke will be set up with a load imposed on it that isn't correct. The manual addresses this by stating that the fork yoke and tubes may have to be hit with a dead blow hammer to free the forks from the yoke.
Here is what I did:
I marked the fork tube with a marker right under the fork yoke on both fork tubes. Then I removed the stem nut and washer as well al the pinch bolts (the forks won't fall out as they are positively held by the upper fork yoke). With the front tire lifted off the ground, I loose the bearing preload nut with a c-wrench about 1/2 a turn or so. This should allow the lower yoke to slide down toward the floor but when I checked the lines a made on the fork tube, the tubes were stuck in the yoke. So, I rapped on the lower yoke and fork tubes with a rubber hammer and this loosed the yoke from the tubes and the yoke slid down, covering the marks I'd made. I then lowered the front of the bike intill the forks compressed some and tightened the preload adjusting nut fully tight. Then, I rapped the lower yoke and fork tubes with the rubber mallet and the lines I'd made reappeared as the yoke slid up further into the steering head. I raised the front end again to lift the tire off the ground and loosened the the adjusting nut a small amount, rapped the fork and tubes with the rubber mallet and adjusted the fallaway into specs. Then I replaced the pinch bolts and torqued them per specs. The fall away was rechecked and was still in specs. Then I replaced the stem nut and washer and torqued it to 45 lb ft. The fallaway was significantly greater than it was prior to torquing the stem nut. I'm guessing this is normal.
I tested the bike using a lot of aggressive front braking and no clunk was heard or felt. I think I would go through the front end as I mentioned first before I'd run the torque up to 90 lbs ft. Of course, if a service bulleting proves me wrong, then I apologize in advance.
Frank