The repackaging scenario you have outlined can be effectively addressed by following these steps.
1. Run the 'Repackager' and launch the 'Repackaging' Wizard.
2. Select 'Snapshot' as your method of repackaging.
3. Select 'Multiple Steps' as your snapshot method.
You would generate your initial snapshot on a clean system,
run the various installations, and then 'analyze system status changes' to generate your base INC file. At which point, you can use the 'Repackager' to complete the process of building the initial ISM or MSI file.
Allen Saxton
InstallShield AdminStudio Development