There's no automatic project-file conversion, but AdminStudio's Repackager tool will let you capture the changes made by your existing setup and turn them into a (pure) MSI project, which you can subsequently enhance with InstallScript and other types of custom actions...
(If you do decide to use InstallScript MSI, see InstallShield KB article Q108166 at
http://support.installshield.com for information about deploying that type of project without needing setup.exe...)