Wonderful,
If you manage these customers with groups you can run the VBScript that will do an AD lookup on their groups. You could execute the various MSI's based on the customer group membership.
Build a Case Statement
Case "GroupWhatever"
CreateProcess "msiexec.exe /i \\whatever.msi /qb", wait
Next
You can run this at the end the MiniSetup.
Hopefully this helps.
You can get some AD/WSH at "http://www.winscripter.com/wsh/"