Some PC-98s came with an OEM version of Windows that was basically slapped onto a cd and copied to the HDD when needed.
To restore it, you have to use the boot floppy the CD comes with (as these systems never got CD boot) and it should do all that nonsense on its own.
...That is, if you have the original HDD.
See, the tool NEC uses to determine the disk size works by returning an error code, and it's compared to a table in the restore utility. Using a disk of a different capacity than the one your machine was expected to have will trip up the whole procedure. Ah, the pain.
Thankfully, there is a tool available (mirror) that lets you overcome the slight limitation, and let you enter the setup utility. On top of that, in case you do not have a restore floppy, this will let you generate one!
Download and decompress the patch, insert the original boot floppy (or a working copy), run the utility and it will do the necessary changes automagically
Alternatively, insert a blank 1440k disk to have the tool create a new floppy. It is assumed that a working DOS installation is present.
After that, if you have already a partition layout, a quick jump into the custom recovery submenu will net you the option to skip partitioning (a good idea for disks larger than 1GB!) and hopefully you can restore now.