Hey there! Sorry for the late response but there’s been a bit of a lull in time and motivation but hopefully things will pick up now.
To get a Win3.1 installation shown under “[ Run System Shell ]” working, make sure you put an installed Windows 3.1 into a ZIP file and store it into the “System” folder of the care, then change it to a .DOSZ extension, for example “Windows 3.1.dosz”. Inside that ZIP you should minimally have a “WINDOWS” folder with things like WIN.COM, WIN.INI, a SYSTEM folder and many more files.
When launching “Windows 3.1” via the [ Run System Shell ] menu it should automatically launch the C:\WINDOWS\WIN.COM but you can additionally add a “WINDOWS.BAT” into the root of the .DOSZ file with custom launch commands. For example you can have a WINDOWS.BAT that contains “windows\win /b” to start without showing the Windows splash screen.