After some messing around with Adobe Audition and trying to remember some engineerin mathematics I figured out to solve my problem!!
Here's how I did it (this is for Adobe Audition 1.5, but I'm sure this could be adapted for other software) and what I started with::
1. Copy right channel to a new mono wav (right clicked -> copy to new).
2. Effects -> Amplitude -> Normalize -> deselect normalize and DC Adjust to -100%
You should now have the bottom part of the wav cut off, leaving only the positive values:
However DC is centred around -100% so it needs to be moved back up to 0%. If you DC Adjust back to 0% with Adobe Audition it gives components below DC that we don't want:
< - Rubbish!!!
So instead:
3. Copy to a new mono wav (right clicked -> copy to new).
4. Effects -> Amplitude -> Normalize -> deselect DC Adjust and normalize to 0%
5. Effects -> Amplitude -> Normalize -> deselect normalize and DC Adjust to +100%
This give you a DC level at 100%. This can now be added to the wav obtained after step two:
6. Copy
7. Edit -> Mix paste... -> Overlap (Mix) -> 100%
You should now have something like this:
This can now be normalized to 100%:
Now all you have to do is go back to the original right channel and repeat the process to get the bottom half:
8. Copy right channel to a new mono wav (right clicked -> copy to new).
9. Effects -> Amplitude -> Normalize -> deselect normalize and DC Adjust to +100%
10. Copy to a new mono wav (right clicked -> copy to new).
11. Effects -> Amplitude -> Normalize -> deselect DC Adjust and normalize to 0%
12. Effects -> Amplitude -> Normalize -> deselect normalize and DC Adjust to -100%
13. Copy
14. Edit -> Mix paste... -> Overlap (Mix) -> 100% with wav from step 9.
This should give you something like this:
You can then use Edit -> Mix paste... -> Overlap (Mix) -> 100% to mix the two halves together:
This can be then copied back into the original stereo wav and the left channel normalized.