Synchronizing audio AFTER in the timeline

Question

Is there any way to sync audio to a clip AFTER it is in the timeline?
Here's what happened in my case.
I have video clips with embedded audio on them. As I was editing with them, I noticed that the audio levels were low.
I now have the stand alone audio from the recorder that has MUCH better levels recorded on it, but I cannot find a way to sync it to the clips I already have in my timeline. Is there any way short of syncing them, and manually finding the in and out points again on the newly created "synchronized clip" and doing a replace edit? Seems like a lot of work and not very precise. Can I in any way replace the audio married to the clip with the new audio and have it sync without creating a new clip?
Another question for the audio guys. Would adjusting the "Loudness" setting on the original clips to increase their levels lose me quality over replacing them with the audio files from the recorder?
(Our setup on set, btw was a Fostex recorder and boom mic recording to CF cards, and audio was feeding out of that into our F900 camera (so all of the clips have sync sound as well. The audio that hit the camera though, is significantly quieter than the individual sound wav files off of the Fostex)
Hope this makes sense, and thanks!

Answer 1

You said ...
Another question for the audio guys. Would adjusting the "Loudness" setting on the original clips to increase their levels lose me quality over replacing them with the audio files from the recorder?
(Our setup on set, btw was a Fostex recorder and boom mic recording to CF cards, and audio was feeding out of that into our F900 camera (so all of the clips have sync sound as well. The audio that hit the camera though, is significantly quieter than the individual sound wav files off of the Fostex)
I will let the other guys address the syncing of a standalone audio track to your video.  There are many ways to do that, and I do that all the time just by aligning the waveform features then pulling the video audio part down to -96dB. You could take all that into a compound clip afterward ... But ...
Regarding the question you asked above.  You Fostex will usally record much better audio than any camera audio circuitry.  I use standalone Tascams to record audio then marry it to the video afterward ... makes a much better experience for the viewer. Your audio level on the Fostex, being much higher in level, will help things, but I still use Loudness on dialog clips.  I don't do anything with commercial music tracks because they have already been maximized for loudness and mixed for proper dynamic range and limiting and compression, etc.
In general you will probably like your audio if you (1) apply loudness, (2) change the volume level slider in inspector to make your timeline audio waveform to where it just rarely touches red peaks ... this usually means the level is around +1dB on the volume level.  Then, make sure you have only the channel selected in your Dual Mono settings under the audio tab, which has an actual audio waveform.  Uncheck the one that does not have a waveform if this applies to you then recheck your volume levels.
Finally, (3) pull over the Adaptive Limiter form the audio section of the effects browser onto your clip ... use it's default settings.  This will add a soft-knee roll off to your louder peaks while leaving the lower features untouched.  I prefer this method to compression because limiters to not boost the noise levels as much as compressors do.  Then, to end up, simply check the volume levels for the whole thing again to make sure you are not above 0dB to +1dB.
If you have special requirements for voices and dialogue, you can use the audio enhancements section and the little EQ icon on the right to open up an EQ feature.  Select 31 band instead of the default 10 band setting then do the following: Increase 3,100Hz by about 6dB to add a degree of excitement to the speaker's voice.  Roll off every frequency below 100Hz by about 3 to 4 dB to reduce the "mud" and rumble.  For a male speaker, boost 250Hz by about 3dB ... for a female voice boost 350dB instead.  Then boost 20KHz to add presence to the audio. 
This is probably a lot more than you need, but you will end up making your audio almost as good as it can be by following these basic principles.  Your mileage may vary 
Best wishes.