Are you sure you set up the masters/slaves the right way (just checking...
)? You should be able to use the grub boot loader with no problem... Is your second HDD detected by the BIOS? If not, the problem is in the BIOS or the hardware. You should check wether the BIOS auto-detects your hard-drives....
If it does, boot from the MDK10.0 CD (or floppy if the CD isn't bootable), press F1 at the first screen and type rescue. You should see a menu on a blue screen (this reminds me of something, but I can't put my finger on it...
). You should be able to boot your installed system from the menu (or at least this is what I remember). If not, choose "reinstall boot loader", "Mount all partitions under /mnt" and then "Go to console"
Type "
cd /mnt" to get to your partitions and then "
ls" to display the contents of the mnt directory, hopefully listing both the windows and your linux partition. If from ls you see dirs like "bin" "dev" "etc" "boot", that means it mounted your linux root partitions in "mnt". You should have another "mnt" directory here so type "
cd mnt" and "
ls". As you are using MDK10.0, you should see directories called win_c, win_d, a.s.o. CD to one of the directories ("
cd win_c") and list the directory using "
ls". If you see all your files, everything is in place, all you need to do is configure your bootloader.
Because you reinstalled your boot loader, you should reboot from the hard-drive (usually the one where you installed linux) and see if the lilo screen shows up (a little colorfull menu with your OSes). If it does, try to boot each system.
Plus, you should give a little more detail about your BIOS config...