If anyone knows how to do this with Audition it would be hugely appreciated.
Here's how i do it in Audition 3.0, but I think it's the same in 2.0 . First make sure you're working with 32bit files to minimize editing artifacts. Go to Effects>Time Pitch>Stretch(process). You can stretch or shorten a file using the
Ratio which is a % of the original file length.
To figure the % you need to shorten it by you have to go into the
Multitrack section. I line up the two files at or near the beginning of the recording. It's real obvious if you listen to the vocal banter between songs to get the echo out. Then go to the end of the two tracks - you should be able to
see how much they are out of sync. Now just highlight and measure that difference which is usually going to be in so many thousandth of seconds, but don't worry about the measurement length look at the begin and end points of your measured difference. This is going to be in H:M:S format which you will need to do a little math to convert the entire two files to seconds. By dividing the larger file into the smaller file you'll get the ratio of the difference between the two.
Now back to the Stretch process select the longer file and apply that number (usually 99.XXXx) to shorten the file making sure to enable
maintain pitch. It can still be little bit of trial an error because you are correcting to a point that may not be at the end of the show thus not giving you a fully accurate % amount. So if the two files still don't sync up then experiment with slightly higher number for the "small x value" at the end of the 99.XXXx number and go back and redo the stretch process again from the original length file. I'd be very hesitant to stretch the same stretched file again.