Well, one way would be to go to the fonts folder in Win98 (first) and select all of them. Then copy them to another folder.
Zip this second folder and burn to a CD.
Go to win98 SE and create a new folder. Unzip the fonts to this.
Then in Win98SE go to the fonts applet in the Control Panel and choose install new font and point the wizard to the folder just created.
Can you explain a little what went wrong when trying to copy the files? It might be that some are system fonts and you tried to move them rahter than copy them.