If you reinstall Windows 9x from MS-DOS (not from Windows), maybe the following experiences can be shared:
Firstly, start the computer to MS-DOS. You can start the computer using a Windows startup disk or an MS-DOS startup disk, or a disk that can start to MS-DOS created through other ways. Before doing this, you should know what file systems you are using for your hard disk volumes. For example, FAT12, FAT16, FAT32 and NTFS (Windows NT file system, used by Windows NT, 2000 or XP). FAT12 is available only for volumes that are smaller than 8MB. FAT16 can be applied on volumes that range from 8MB to 2GB (sometimes up to 4GB is also possible). FAT32 can be applied on volumes that range from 512MB to 2TB (2048GB). NTFS can be applied on a much wider range, but cannot be recognized by any existing MS-DOS systems. MS-DOS 5.0 to 6.22 and 7.0 (attached to Windows 95) can recognize FAT12 and FAT16. MS-DOS 7.1 (attached to Windows 98) and MS-DOS 8.0 (attached to Windows Me) can recognize FAT12, FAT16 and FAT32. There are more limitations to MS-DOS 7.0 and earlier: They cannot use hard disk space higher than 8GB, that is, if your hard disk is larger than 8GB, the part over 8GB cannot be used by them (MS-DOS 5.0 to 6.22, and Windows 95). So, you'd better use an MS-DOS 7.1 or an MS-DOS 8.0 startup disk, that is, a Windows 98 startup disk or a Windows Me startup disk.
If you need CD-ROM support for MS-DOS, and you are not using a Windows startup disk, you can use a versatile ATAPI CD-ROM driver IDE.SYS which can be found on the web. Then, use MSCDEX.EXE to create a drive with the CD-ROM driver. For detailed information, see my AUTOEXEC.BAT page. If you don't want to download IDE.SYS, you may try OAKCDROM.SYS which can be found in %windir%\COMMAND\EBD, where %windir% is the installation target directory for Windows 9x (if you can find an installed Windows 9x on your or your friends' computer). Usually, if you have a genuine Windows 9x pack from Microsoft, there should be a Windows startup disk so you don't need to make it yourself. Some computers support booting from a CD-ROM. Maybe your computer does. Thus you can start your computer using a CD-ROM. Notice that booting from the CD-ROM still requires a CD-ROM driver to support your CD-ROM drive. If no CD-ROM driver is provided by the startup CD-ROM, the CD-ROM drive will be unable to be accessed after starting up.
Microsoft also suggests that you copy all files in the Windows installation directory to your hard disk, and then run the installation program. You need to speed up disk access before copying the files. The way to speed up disk access is running SMARTDRV.EXE. The executable can be found in the the Windows installation directory. You can run it without parameters, also you can run it with a parameter specifying disk cache size in KB. By default, if you have more than 6MB extended memory, SMARTDRV allocates a 2048KB disk cache. If you want the disk cache to be larger, you can enter a larger number as the parameter of SMARTDRV.
Run SETUP.EXE to start the installation. By default, SCANDISK will be automatically run. If the computer is started with an incompatible version of MS-DOS, SCANDISK may fail. So it is suggested that you start the computer with a compatible version of MS-DOS (7.0 for Windows 95, 7.1 for Windows 98, 8.0 for Windows Me). An important notice: If you use MS-DOS versions earlier than 6.22 to start the computer, you should not run SCANDISK for those MS-DOS systems because that version of SCANDISK is not compatible with long file names (long file names are supported by Windows 95 and higher). Neither should you run CHKDSK for MS-DOS 6.22 or earlier.
Before installation, you can repartition the hard disk using FDISK or format volumes on the hard disk using FORMAT. See those related pages on my site for more information. Of course, you can use Partition Magic for MS-DOS, or some other tools to make such operations. Notice that if you use Partition Magic, you can specify your preferences whether to check the hard disk for bad clusters. Checking for bad clusters will be more secure but will take more time. The default setting is that Partition Magic checks for back clusters.
If your existing Windows system has been infected by one or more viruses, and you have an anti-virus tool installed, you may scan for viruses using the tool under MS-DOS. It is safer scanning for viruses under MS-DOS because Windows viruses cannot be run in MS-DOS.
Sometimes SCANDISK will report long file name error (maybe because of file operation in pure MS-DOS; MS-DOS for Windows 9x doesn't leave such errors), and SCANDISK cannot repair that error. Then the SETUP program doesn't let you go on with the installation. At this time, you can run SETUP again with a switch /IS, which can make SETUP skip the SCANDISK process.