I'm not sure if the .exe file you would download would actually write it to a cd because it specifically asks for a floppy disk during the instructions, but you can give it a try...then set your bios to boot from the cd as the first boot device if it will write to the cd instead of a floppy disk.
The W98 cd is also bootable and you might be able to use that cd to boot with and see if the beginning screens give you the option to format the drive.
One other option is to go into your current C:\Windows\Command folder and click Edit, click Select All, and the burn all of those commands to a cdr and use that disk to format with since one of the commands is format.exe The key is to change your bios to boot to the cd first so you get cdrom support. The following instructions show you how to get the real mode drivers onto a floppy disk, but it should work also for a cdr....you will have to search your harddrive for the files listed since you can't get them from the actual bootdisk and burn them to the cd and create the autoexec.bat and config.sys files as shown here as well. Then after saving those files, burn them to the cd, too.
How to Use Real-Mode CD-ROM Drivers from Windows 98 Startup Disk (Q190303)
The Windows 98 Startup disk includes a set of generic real-mode CD-ROM drivers. These drivers work with most Integrated Device Electronics (IDE) ATAPI-compliant and Small Computer System Interface (SCSI) CD-ROM drives.
This page describes how to configure your computer to use the real-mode CD-ROM drivers from the Windows 98 Startup disk. This may be useful when you need real-mode drivers for your CD-ROM drive, or when you are unable to configure the Windows 98 protected-mode CD-ROM drivers to function correctly. This method will put all the cdrom drivers on your harddrive and show you how to edit the autoexec.bat and config.sys files so that the real-mode drivers for your cdrom load up without the bootdisk.
Determining If the Real-Mode CD-ROM Drivers Work:
Before you configure your computer to use the real-mode CD-ROM drivers from the Startup disk, verify that the drivers work with your CD-ROM drive. To do so, follow these steps:
Restart your computer by using the Windows 98 Startup disk. On the Startup menu, choose Start Computer With CD-ROM Support .
Insert a CD-ROM into the CD-ROM drive.
Type DIR (drive letter): and then press ENTER, where "drive letter" is the drive letter for the CD-ROM drive. Note that the CD-ROM drive letter may be one letter higher than you expect.
If you can retrieve a directory of the CD-ROM, the real-mode drivers work with your CD-ROM drive. If you cannot retrieve a directory, you must use the drivers that are included with your CD-ROM drive.
Using the Startup Disk Real-Mode CD-ROM Drivers:
To configure your computer to use the real-mode drivers from the Startup disk, follow these steps:
If you have not already done so, restart your computer by using the Windows 98 Startup disk.
Create a new folder on your hard disk and then copy files to the new folder. To do so, type the following lines, pressing ENTER after each line:
copy aspi2dos.sys c:
copy aspi4dos.sys c:
copy aspi8dos.sys c:
copy aspi8u2.sys c:
copy aspicd.sys c:
copy btdosm.sys c:
copy btcdrom.sys c:
copy flashpt.sys c:
copy himem.sys c:
copy oakcdrom.sys c:
copy c:\windows\command\mscdex.exe c:\rmcd
There should be 11 files in the new folder.
Make backup copies of your Autoexec.bat and Config.sys files (if they exist). To do so, type the following lines at the command prompt, pressing ENTER after each command:
copy autoexec.bat autoexec.sav
copy config.sys config.sav
Type edit autoexec.bat , and then press ENTER.
Add the following line to the Autoexec.bat file:
lh c:\rmcd\mscdex.exe /d:mscd001
On the File menu, click Save , and then click Exit on the File menu.
Type edit config.sys , and then press ENTER.
Add the following line to the Config.sys file:
NOTE : If the Himem.sys line already exists, do not add the line above.
Add the following lines to the Config.sys file:
Now press ALT and press F (this opens the File menu), press S (this will save the file), press ALT and press F again, and now press X (this will close the file) You will need to do this for both the autoexec.bat and the config.sys files after you edit them.