The kmr barrel nut is quite soft metal. Even with great seating, the wrench tends to deform the small barrel nut notches, and that interferes with the rail sliding on. It's better to have help with one person keeping the wrench flush. If mildly marred, try using a small, lightweight hammer to peen the surface flat, or V7 Weapon Systems sells a titanium barrel nut thats a bit sturdier.
As for install, try using a small rubber/plastic double hammer. Tap evenly on the front or rear ends of the rail to replace and remove, respectively. The taking off bit is hard as mallet strikes have to be done alongside the upper. It might take several tries to align the antirotation notches, and if I recall correctly, the assembly instructions even call for using flat metal gauges between the upper and rail for seperation by a cunt hair.
As for the tightening nut, do not force the screw through the hole. It will slip through without tension when the rail is at the correct position. Readjust the rail -- usually more forward because of that gap between the upper and rail.