It is possible. When setting your flash drive as a boot disk make sure you use an image of your Windows CD. You should be able to boot right into DOS from your flash drive and install where-ever from there.

You can try to copy everything from windows 98/me iso onto flash drive, and try to boot using ploplinux i linked before. Maybe it will work. But if you cant use CD drive you are out of luck, you cant boot usb on very old computers. Giulia Siegel Im Playboy on this page.

No need to use multiple drives really. Another thing you should be able to do (feasibly) is try mount your cd drive from your dos bootdisk (what I'm assuming is on your flash drive).

I did the same thing years ago for kicks just straight from a flash drive. Killed some time. Hope that helps, cheers.