Ok, first, the "MS-DOS" that you want to use is "MS-DOS 7",
"extracted" from
Windows 98SE. This is easy, just find a 98SE system and format a bootable
floppy. The utilities are in C:\Windows\Command of the 98SE system.
[additional MS-DOS utilities are on the Windows 98SE CD]. This version of
MS-DOS ***WILL*** recognize FAT32 partitions. Also, there was an update to
FDISK in May of 2000, you want to get that, it's available from the
Microsoft web site. It will recognize drives up to 137 gigabytes.
There is no easy way to manually install, but you can boot from a DOS
bootable CD and run SYS from that. After you make the "MS-DOS 7" floppy
(above), use that floppy as an "image" in making a bootable CD.
That should get you where you want to go.
[Note, the full set of DOS utilities won't fit on a 1.44MB floppy, so be
sure to put them on the CD so that you have a place to copy them from.]