Welcome to Windows 9x and later. In the old Dos?Windows days, xcopy would have worked fine. Unfortunately, we now have long file names that will be corrupt if you just boot to a DOS 6.x boot disk and files that will be in use and not copy if you attempt to boot through Windows.
Get a utility called Ghost. Ghost will copy the drive sector by sector to an image file. Once the file is created, you can use ghost to restore the file to the new hard drive. I have never tried this, but I believe you can do a hard disk to hard disk copy, too, if you prefer. Either way, you will boot to a bootable dos disk. (Bootable win 9x disk is fine, too) Run ghost (you can copy ghost.exe to either drive, or just copy it to the floppy. Once you are at an A:> prompt, type ghost (or c:\ghost or wherever the file is located) and the program will load. here you can choose clone disk to disk, disk to image, or image to disk. If you use the image file, use disk to image. Pick the partition you want to copy, give it a filename and create the file on the other hard drive. (You can't restore an image file to the same disk you are reading the image from, nor can you save an image file to the drive you are cloning, and a name such as Cdrive.gho is very clever!) Once the image file has been created, you will need to copy that image file from D: to C:. (You CAN use xcopy for that!)
Once the clones disk AND the image file are on the same drive, shiut down, swap the jumpers so your new drive is primary and the 6GB is slave, and reboot to the dos disk again. Run ghost, but this time restore image file to disk. Pick the new drive as your destination drive, pick the image file from the 6GB drive and let it go. when it's complete, disconnect the D: drive cable and reboot. You should see the same setup you had before, except instead of a 6GB drive you have the new drive. If this did not work, you can fdisk the new drive, swap the jumpers back between the drives, and you're back to where you were when you 1st started.