You will have to manually change the 98 line, unfortunately. (I don't understand how this happened, though.)
multi(X) is for IDE (or SATA) port number X. rdisk(X) is for raid drive. The other two you already know. the \WINDOWS part should be whatever the Windows folder is on its root drive (%windir%).
So if you have both the hard drives on the same port, it should look like this:
multi(0)disk(1)rdisk(0)partition(1)\WINDOWS="Microsoft Windows 98SE" /fastdetect
If the hard drives are on different ports, that line should look like this:
multi(1)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows 98SE" /fastdetect
Also, I noticed that /fastdetect is spelled wrong so if that is directly copied from boot.ini, then that might be part of the problem.
For more information about your particular hard drive configuration, right click My Computer > click Manage > Storage > Disk Management.
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