I know there were updated versions of FDISK as well as other dos based utilites over the years.

Is there an updated Windows 9x boot disk floating around with all the latest and greatest files?

Did yous try http://www.mdgx.com ?????? Thats where i started 118 months ago and still do....

Get http://www.mdgx.com/files/BHDD30.ZIP and KB311561, still available from Microsoft, and you've got all that's necessary to build one based on your EBD disk.

BHDD30.ZIP has ME Scandisk for DOS, updated FDISK and FORMAT. It was created by Maximus-Decim some time ago, but is much less generally known than his other releases... Yet, it rocks, as M-D's releases use to do. KB311561 has the latest IO.SYS. HTH

Wouldn't dropping said files into the EBD directory also produce boot floppies with the updated utilities on them? It does require changing the ones in the cabinet though as well, right?

(crosses fingers and hopes that was the directory used to pull files for created boot floppies)

I have always used the custom (no ramdisk) bootdisks from www.bootdisk.com, you can drop in there all that you want, and there is no cab file to update.

Well, yes. KB311561 a.k.a. Q311561 is still available from Microsoft (link), and Petr (link) localized it to lots of languages, in case you ever need a localized version, because Microsoft put the English version, by mistake, in most of the localized versions they offer. On applying KB311561, it'll update both the root directory and the EBD directory. Likewise, by applying BHDD30e.ZIP it'll update everything, but the EBD.cab inside the EBD directory. That you'll have to update by hand. You'll need Microsoft's CABARC utility to do so (link). And I just found out I was mistaken: you'll have to grab the DOS version of scandisk.exe from Win ME from inside MDGx's package SCANFRAG (link), because only the windows version is present in BHDD30e.ZIP. But having installed BHDD30e, I don't think you need to actually install the SCANFRAG package (unless you want to: you may not want all the updates it installs... myself, I don't like both meconfig and regenv32, and stick to the older msconfig), get it just to grab scandisk.exe from inside it.

Not exactly, the EBD folder is only used to make EBD floppies when you invoke bootdisk.bat file, the folder you are wanting to use instead is the Windows\Options\Cabs folder provided you have one and have moved your cab files there along with applying IO.SYS update KB311561 AND you have
[HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Setup]
"SourcePath"="C:\\Windows\\Options\\Cabs"

in your registry pointing the Add/Remove Programs|Startup Disk creator to the replaced files. If a file can be found in a cab folder already expanded, it is used directly instead of the file compressed inside a cab somewhere, so this replacement technique works out perfect for us this time around.

It does however require changing the ones in the EBD cabinet file just as you suspected.

Universal Multiboot Disk launch botch families of Windows NT5x: 2000, XP, 2003 server and Windows 9x: 95, OSR2, 98, 98SE, ME.

2 in 1 single floppy . Bootable floppy disk for an NTFS or FAT partition in Windows XP & MS-DOS Startup Disk version 8.0 from Windows XP .

C:\bootsect.dos="WINDOWS 98SE/ME" for floppy just indicate DOS bootsector root directory.
Installable File System (ifshlp.sys) driver added for launch Windows 9x
Windows ME's FDISK is limited to creating partitions with a maximum size of 512 GB