you cant just copy over windows from one system to another without special software because there are many files that simply wont be seen.
You need to 'ghost' it using norton ghost.
Is the bios setup correctly on the new machine? does it say you have a second floppy?
have you partitioned and formatted the new drive in your machine?
use your old system and format a floppy 'system' disk. Now from your windows\command folder copy
fdisk / format / sys to the floppy.
Boot using this floppy in your new machine.
Now run fdisk and create a partition/s
Now run format on the new drive
Now at the A> prompt, type SYS C:
Your hard drive will now boot to the c: prompt
All you need to do now is create an autoexec.bat file and config.sys to use your cd-rom drivers and you can install windows 98
Dont bother using himem.sys etc, when you go to your D: drive, go into D:\WIN98 and type XMSMMGR and this will manage the memory perfectly