I can't imagine that what you're suggesting is significantly different from what the other cloning tools are doing.

However, it might be worth a shot to try copying only the Windows partition:

Boot into Linux. Partition the new drive into a single partition using fdisk or some equivalent. Set the partition type to whatever it is supposed to be for your version of Windows and filesystem. You can use fdisk to inspect the old drive for this information. Make sure that you mark that partition active. Then "cat /dev/oldx > /dev/newy" where "old" and "new" are "sda", "sdb", "hda", or whatever, determined by inspecting the hdparm output or the contents of the /sys/block... files Mark pointed at in a later post, and "x" and "y" are the partition numbers of the old and new partitions on those drives. That sounds complicated, but it should be reasonably obvious once you're there.

You can also download a trial version of Symantec Ghost to see if that would work better than the other cloners.