I had the same problem looking for old disk imaging software. After many test and issues I ended using the simplest solution: 7zip. It is fast (there is 0 compression), portable (DOS, Win9x, Win10, Linux, macOS, etc) and most important it is easy to check what's inside, eg. just to get one file like autoexec.bat. You can do the backup straight on the machine with a floppy or by card reader on modern PC and it will work cross platform.
My routine is:
1. install Win98,
2. 7zip WINDOWS and Program Files folders (or whole C: drive),
3. install drivers, software, etc,
4. when something goes wrong, delete WINDOWS and Program Files folders and extract them from backup
5. repeat from 3