I tried using a type 39 custom action but this was only partially successful in that some but not all of the child installation was removed. Reading through the documentation again however, it appears that you can only use this method for uninstalling if you installed the product in the first place. (To quote the MSI help file: "The Type 39 custom action cannot be used to reinstall, or remove any product that previously was installed by any other means").
I cannot install the base product myself because it requires that the MSI is only launched from setup.exe (If I double click on the .MSI file it simply pops up a message box indicating that the product should be installed by running setup.exe). I can't run setup.exe because of the restrictions on running nested installations in the execute sequence mentioned earlier.
I don't believe that I'm asking too much of an install product. I could install and uninstall my product using a batch file and then I wouldn't have this problem.
I've been writing software for over 12 years now and this is without a doubt the most frustrating product I've ever come across!!