"Pure dos" really doesn't offer any benefits over MS-DOS mode in Win9x and I would strongly suggest forgetting the whole thing. You can always use a boot floppy if you really need "pure dos" for something or other.
Otherwise, if your hard drive is FAT16-formatted, then just install MS-DOS before installing Win9x. Then you can press F8 when booting (when the "Starting Windows ..." message appears) and select "Previous version of MS-DOS" from the menu.
If you are using multiple primary partitions on the same drive, then I suggest manually toggling the Active partition using a utility like gdisk rather than bothering with a boot manager.