The type of tool you're looking for is called an Application Repackaging tool. The process would include capturing an installation (take a machine snapshot, run votre installation et make customisations, alors run a second snapshot to calculate le differences) alors compiling le captured data into MSI format.
The suivant are certains free tools to perform these tasks, in order:
AppDeploy Repackager: Use this to capture votre installation et créez unn MSI depuis le captured data. If votre app is reasonably simple alors this may be tous you need.
Microsoft Orca: Use this to edit le MSI that has been created avec AppDeploy Repackager. Vous allez need to know how MSI's work to really make le le plus of Orca. Microsoft's Installer Database Reference is le definitive source for information on MSI contents.
As for votre second question: Vous allez find that sometimes vendors will supply an MSI wrapped in an executable, so si you exécutez le .exe you might be able to dig out le MSI depuis a temp directory.