How do you synchronize an audio file - which has no gaps - pause with a video file?

It's possible to do the bulk of this in Audition, but you won't be able to finish the job in it, because Audition doesn't print audio files back to video any more - that's a job for Media Encoder.

The principle is very simple. You start a Multitrack session (for a video, a 48k session at the default bit depth is fine) and go to File>Import>File and find your video file. Now drag it from the files panel onto the top track in your session, and it will open up a video reference line, and put the original audio underneath it. That's your reference. Now you import your new audio file, and place that on the timeline underneath. Line it up so that it starts in the correct place. At the point where it goes out of sync because of the pause, right-click on it and find the 'split' option (Ctrl+K). Now grab the audio on the right hand side of the split, and drag it to the next place you want it to start, after the pause.

When you've edited the whole soundtrack, you have choices: if you want (and you probably ought to, just as a safety copy) you can mix down the audio result to create a new file - this is the one that's in sync. The actual audio from your original file hasn't been touched - Multitrack is non-destructive and works 'virtually', so you need to do this to create a real file. Whatever you do, save the session, though - this is your route back to redoing it if you need to.

But you don't have to save the file if you don't want to - just select Export>Export with Adobe Media Encoder (you have to have this installed - won't work otherwise), and you'll be presented with export options once the Encoder's opened. And that's how you get the video and audio back together - it does this directly from the Multitrack screen. Here is a picture showing the basic principles of all of it:

I just edited the video's original sound track so you can see where the splits are. On yours, you'd leave that audio track alone, and place your new on on the track below, and split it there appropriately. The other thing to note that I didn't mention is that you will have to hit the 'mute' button on the original sound track before exporting, or you'll end up with both on the video - probably not what you want. That's the one that says 'M' in the track controls.

It's the same principle as above for creating any other versions - just line them up against the original video on the first track and mute everything you don't want in the result.