Do you have the front end lifted? If not, that's the problem. The weight of the bike causes the bottom triple to flex slightly, and it throws off the alingment of the top of the forks relative to the stem.
Use a headstock lift on the front (not a fork lift), or a jack under the engine to relieve the pressure on the bottom triple, and the top will slide right on.
Use a headstock lift on the front (not a fork lift), or a jack under the engine to relieve the pressure on the bottom triple, and the top will slide right on.