Repackaging is very similar to other Adobe Applications. In Wise Package Studio, perform a default capture on a clean machine.
Edit the package, looking for extraneous files and registry entries, and move the shortcuts if needed.
Perform a compile, making sure to set the build option to external cabs. This allows the MSI to load mush quicker than if it was a single file compile.
There are three INI files you will need to be concerned with. One called Maker.INI. There are two of these, one under the user profile (delete this one) and one in the main program directory. Due to the way WPS likes to interpret INI files, I recommend adding this as a regular file instead of using the INI creation category.
The third INI file is in the program directory, under the FMINIT folder called Fbtoolbr.ini. I recommend adding this as a regular file as well. It controls the buttons that appear in the default configuration of the toolbar. There are some INI files created in the plug-in directory as well, but these seem to be fine.
Once these three were addressed, the application installed and uninstalled fine. You may also want to add an entry to remove the FrameMaker folder on uninstall. Using the program, it creates a few files in the main program directory, and these are left behind on uninstall.