Never looked into it but the source for the setup is included with VB so it is possible to modify it to suit your needs. I have modifed the sections that read the ini file and create shortcuts but that is about as far as I have gone with it.
Assuming you installed in the default location the source code would be located at
C:\Program Files\Microsoft Visual Studio\VB98\Wizards\PDWizard\Setup1
I always used InnoScrip and InnoSetup. A member over at VBF used to give i away (for donation) unitl he wrote it in .Net, and made it 1000% faster. Now, it's a few bucks. http://www.randem.com/randemsystems.html