Depending on the drive in your Windows 98 machine, there's a small chance that it may not be able to read CD-R's. [link|http://www.osta.org/technology/cdqa6.htm|This page|new_window=true] offers an explanation of the differences between different types of CD media. It's also worth confirming that the CD-R disks (they aren't CD-RW, right?) are good. Over time, optical media goes bad, and if these disks are decades old, they may no longer burn reliably. If you have spares, it may be worth a shot re-burning at the slowest possible speed and validating the burn afterwards.
For the flash drives, you may be able to get it working on the old machine if you make sure that it is the FAT32 file system. If you have an old and small USB 2.0 drive, that would probably be preferable to a large modern drive.