The Installer
class based custom actions do not integrate well with the Windows Installer. The Visual Studio Setup Projects created a workaround to shoehorn them into an .MSI file but that was never the ideal situation. The WiX toolset provides true support for managed custom actions using the DTF
framework.
I highly encourage you to take a look at the DTF Documentation
shortcut provided with the WiX toolset. It has decent walkthroughs and I expect you'll be able to port your code pretty easily plus you'll be able to integrate far more with the Windows Installer.