本文发表在 rolia.net 枫下论坛如果我判断的不错的话，你应该是98的硬盘为master, 2000的硬盘为slave. (因为你说你的98上的boot.ini文件大小为0）。
if it's ture, please follow,

prepare
Start your win98 only:
1. boot from floppy (windows 98).
2. use sys c: transfer your system to 98 harddisk
3. rewrite you MBR.
Then study your windows 2000 only
1. change 2000 harddisk boot.ini file,
and one lines under
" multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="windows 2000" "
the line is
" multi(0)disk(0)rdisk(0)partition(1)\windows="Windows 2000 1" "
only change rdisk(1) to rdisk (0).
2. reboot your computer and confirm there are more option in the startup menu.
3. you can startup your computer by the default one. If you select one which you added will fail.
4. shutdown your computer and connect your harddisk as master.
5 start you computer and try the one you added to start your computer. If you can start your comptuer. That's ok.
6 If you can start your machine by the second one, you will login and change the boot.ini file "default" to the new one.

Pay attention, never delete the old one because you can reconnect your harddisk to slave and login by the old one. If there anything wrong and you delete the old one, you will never login to the windows 2000.

If you can success do it, you can connect your 98 as slave disk and add new line in the boot.ini as follow:
" multi(0)disk(0)rdisk(1)partition(1)\WIN98="win98"
and try to slect the new one to start it.

Pay attention, the configuration "multi...." is copy from my disk, so it maybe different than your. if you understand it, you can try this way. If you don't understand you'd better to find some article (search "OS loader" in yahoo) to understand it. And then do it. If you have more question, you can mail me.

Pay attention again, this action is very dangerous, so please understand what your do first.更多精彩文章及讨论，请光临枫下论坛 rolia.net