Since you have to swap, it really doesn't matter if you modify the autoexec.bat and config.sys file on the floppy, since you can't put in the CD ROM at this point anyway to access it.
The easiest way is create a bootable CD ROM with the generic CD ROM drivers from a Win98 CD. There is one you can download at http://www.onecomputerguy.com/install/floppies.htm that also has a lot of the basic DOS utils that don't normally get included.
Include on that CD ROM the source files for Win9x.
Then you can boot with the CD ROM in install the OS. You also might want to copy the source files from the CD to the Hard drive and install from there. Then when windows needs and base files or drivers, you won't be prompted to insert a CD. This would be especially helpful if you happen to have the floppy drive plugged in at that time.
The easiest way is create a bootable CD ROM with the generic CD ROM drivers from a Win98 CD. There is one you can download at http://www.onecomputerguy.com/install/floppies.htm that also has a lot of the basic DOS utils that don't normally get included.
Include on that CD ROM the source files for Win9x.
Then you can boot with the CD ROM in install the OS. You also might want to copy the source files from the CD to the Hard drive and install from there. Then when windows needs and base files or drivers, you won't be prompted to insert a CD. This would be especially helpful if you happen to have the floppy drive plugged in at that time.