Hi there,
So you want to capture the uninstaller.
Well, you'll need to change the options to check for deleted files and registry entries to capture an uninstall when running the repackaging wizard.
You could monitor this one if you have an uninstall.exe, maybe check the uninstall shortcut arguments if you have one or look for the program's UninstallString in the registry (HKLM\Software\Microsoft\Windows\CurrentVersion\Uninstall).
Alternatively, use ye olde snapshot method.
Marco