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You don't say what brand of SCSI disk it is, but most new IDE disks come with a software CD from the factory or utilities available for download from the manufacturer's website. This software allows such things such as partitioning and copying a partition from the old disk to the new disk. It does not care what the contents of the partition are. If your new SCSI drive came with a similar CD or you can find the utilities on the web, I would use those tools instead.
Here is what I usually would do when duplicating my install to my spare drive. First boot with knoppix 2 to get to a console root prompt then,
mount /dev/sda2 /mnt/sda2
mount /dev/sdb1 /mnt/sdb1
cp -Rp /mnt/sda2/* /mnt/sdb1/
vi /mnt/sdb1/etc/fstab <----- Changing all sda2 to sdb1
vi /mnt/sdb1/etc/lilo.conf or /mnt/sdb1/boot/menu/grub.lst <------ Making changes for new drive again
chroot /mnt/sdb1 /sbin/lilo -v <----- or for grub
Now for installing the lilo/grub it can get a little complicated unless you want to keep it on the drive you already have it on in which case when editing their config files only change the parts that refer where the kernel is located and just let it install itself into the MBR of the sda drive like it is now (it it?). If you still have problems the output of fdisk -l and seeing which of the config files you are using would be nice.
There is the boot manager (lilo/grub) issue to deal with.
1) The boot loader on /dev/sda must be not changed or overwriten by windows.
2) If the boot manager is lilo them the MBR must be updated to reflect the new boot dir. (lilo -v)
A working live CD would be valuable if anything goes wrong.
And don't delete the linux on /dev/sda before you are sure your system is working right on the new location.
Keep copies of the original /etc/lilo.conf and /etc/fstab just in case.