I don't have the H4N but if you go to a site called dvxuser there would be experienced users of the 5DMkII and the H4N that can help you.
What I've heard is that depending on your framerate (30p vs 24p) you have to set the recording frequency on the H4N differently in order for it to sync properly.
Have just opened a job I did in early July. All the frame rates are 29.97, just like this project. The properties all also identical to this project. Yet all the audio tracks on the earlier job are perfectly synced.
I check the timeline of the new job and the H4n audio is exactly 02:20 seconds slower than the audio it fed to the 5DMII. I am also running a 60D at the same time. Both Canon's audio match perfectly. The 60D is using its camera MIC. Only the H4n is off.
I ran a test today and everything sync just fine. Set up the 5DMII with its audio coming from the H4n. Downloaded both audio from the H4n and the audio video from the 5DMII. The aduio tracks were identical as they should be. I am still baffled as to why the H4n audio was so different on the job. Oh Well.