Did you download dd yet?
extract the dd.exe to c:\
Do you know the physical drive number for the DMS?
Run Disk Administrator (start menu - run - c:\windows\system32\diskmgmt.msc )
Find the drive that has the phtsys and phtdta on it, and note the drive number listed on the left hand side.. it is important to use this number when running the DD command so you don't screw up your PC.
Do you see a file in phtsys in the backup folder called drive-sig-1mb.bin ? Copy that file to your c:\ directory as well.
Eject your old DMS.. Put in the new drive in the DMS case and place the new DMS back in the cradle.
run command prompt (start menu - run - cmd.exe)
Type this command but replace the X at the end of physicaldriveX with the number you found in Disk Managment. VERY IMPORTANT TO GET THIS RIGHT!!!
(typing in the wrong disk number could crash / ruin data on other drives so BE CAREFUL AND BE SURE)
dd if=c:\drive-sig-1mb.bin of=\\.\physicaldriveX bs=512 count=2048
Eject the DMS after doing this.. You'll have to reboot and use the format utilty to repartition the DMS and reformat it (this is the NEW DMS) but it should now work great in any phatbox that has been patched.
If you cannot get the Phatnoise version of the Boot CD or our version of the Boot CD to work, I am quite sorry but you are foobared.. theres no real way I can tell you how to simply reparition and reformat the DMS in any other OS than by using one of those bootable CD roms.
I might suggest if you still have issues with the boot cds that you download vmware from
www.vmware.com as an evaluation, install it.. configure a guest OS of linux with a 256 meg hard drive on it (this is a fake drive that is really a file on your hard drive not another hard disk for real) and then you can redirect your USB cradle and CD drive into the vmware machine and try using it to get around any usb issues you may be having.