|Think about it for a minute. It's not that hard.|
In a separate folder on your hard drive copy from your existing 98 cd all the files and folders you want on your modified cd. Then copy to that same folder all the additional files you want on your cd.
Then get a 98 bootdisk. Delete all its files except for command.com, io.sys and msdos.sys. Or, from a working 98 system do a SYS A: with a blank disk in the a: drive.
Then start your burner software and choose to make a bootable cd. The stuff you want on the cd will be the contents of the folder you copied everything to. (You'll need to choose the individual folders one by one so it'll be as much as is possible like your original 98 cd.) Your burner software will ask you to insert a system disk. Put the bootdisk in and if necessary direct the software to look there.
The 'boot from cd' option that often shows when using a bootable cd comes from a file named jo.sys which is a replacement for io.sys. You can download it and setup the bootdisk to use jo.sys instead of io.sys from here:
But the cd should be bootable without jo.sys. You just won't get the option message. That will force you to always boot from the cd when using it.
I've never had to do this with a 98 cd and it's possible you'll need a config.sys file to load himem.sys. If so, you'll need to modifiy the bootdisk to include that. But first try it without and see how it works out.