MPEG4 audio out of sync (longer audio file than video file)

Good day,

It has been at least 5 years since I was into video editing and today I'm in it again and having some problems.
I would like to know the best way to handle this with the best video quality.
This is my situation:

- I recorded a wedding using a Nikon D7000 that created 1920x1080 23.976 fps MOV files with PCM audio
- I want to upload the edited video in HD on Youtube (with some 'Youtube'-stabilisation and chapters on it)
- I used Pinnacle Studio 14 to edit the videos and export them to a MPEG4 file 1920x1020 23.98 fps video 12000kbit/s audio 128kbits/sec
- My audio is out of sync, I think it is the same offset for the entire video, not increasingly
- I used TMPG ENC Video Mastering Works to import the file and I saw the 'audio' of it was 680ms longer than the video
- Using TMPG Enc, I did an audio offset of -680ms and exported the Audio to a WAV file
- Using TMPG Enc, I opened the video file again and have set the audio to the .WAV file (that has the same length)
- Using TMPG Enc, I did an 'export' to MPEG4 with 1920x1020 23.976fps and 12000kbits/s

That final step is still running and will take another 5 hours.
It seems strange to me that I have to reprocess the entire video file just to have an audio offset on it.
I fear that it will decrease my video quality, are there any better ways of doing this?
What is the easiest or best way, any advices?

Thank you,

djorkaef