I was able to convert PNG files into ICO files (thanks to Turn pngs to one ICO file ), but now I would like to create an icon "bundle" similar to
system32.dll, which contains several individual icons. How can this be done?
You need to build a DLL that contains multiple icons as resources. That can be done from Visual Studio via these instructions. Other Windows development tools that can create a DLL should be able to do the same thing.
This could even been done with the resource compiler (rc.exe) that is included in the Windows SDK and manually creating a resource file.
Looks like this will work as well.
It turns out that there was a Java rewrite of CombineIcons called Icollator, although it still only supports up to 128x128 pixels.
There is a program could meet your requirement. It's GConvert: https://www.gdgsoft.com/gconvert/help/index.aspx?page=HDIODll.htm
But so far, this freeware only support 256x256 size. If you ok with that then you may wanna give it a shot.