This is actually pretty much what I do for a living: we use a combination of batch files driving perl and VB to non-interactively package to InstallShield for Windows Installer. Our experience says to skip the InstallShield part, and go directly with Windows Installer. My goals for this project, at least the Windows part, is to eventually get rid of all the batch files and VB script, and go with pure perl, perhaps with WIX.

We actually use the same perl code to package to RPM on Linux, LPP on AIX, pkg on Sun, and software depots on HP. And I used the same code base to produce an ISMP prototype (which we've abandoned), as well as a few other technologies.

If we continue using Windows Installer, we'll probably use WIX. So that would be my suggestion to you.