Had a few people asking for this and sucess stories with those who have tried it so here it is.
QUICK TUTORIAL FOR UPGRADING HARD-DRIVE AFTER ALREADY SOFTMODDING STOCK DRIVE.
1) Get xboxhdm and extract it to your PC.
2) Use ConfigMagic (or any alternative if you know how to do this) to extract your eeprom on your xbox. It is likely to be in E/Backup/EEPROMBackup.bin. FTP this to your pc, rename it to eeprom.bin, and put it into the /eeprom folder of xboxhdm.
3) FTP into your Xbox. If you can see the contents of your C drive then SKIP this step and go onto step 4. If not, go into your File Manager on your xbox, navigate to e:/ndts and run the default.xbe in there. This will load an altered version of unleashx with full access to C and E.
4) FTP your C and E drives onto your pc and put them in the respective folders in xboxhdm.
5) Run make-iso-win in xboxhdm and burn the iso with alcohol 120% or any other alternative image burning software.
6) Place the xboxhdm CD in your cd drive and then shutdown your PC. Disconnect your PC hard-drive. Connect your new hard-drive to the primary master of your PC and then boot up your computer.
7) When xboxhdm loads up choose option 1, then when it's loaded type 'xboxhd'. Choose option 1 again to prepare xbox hard-drive from scratch. Answer Yes to all the questions and when it is finished hit reboot.

Now xboxhdm will load up again. This time choose option 3, and then once this is loaded type 'lockhd -a'. This will find your eeprom.bin and lock the hard-drive*
9) Your new hard-drive is now ready to put into your xbox and will be an exact mirror of your existing xbox drive but obviously with a lot more free space.
* Sometimes people can have problems with this step as xboxhdm won't detect the eeprom.bin file. 2 workarounds are available for this:
1) If you have a floppy disk drive on your PC then copy the eeprom.bin to a floppy disk. Insert this in the drive and then within xboxhdm if 'lockhd -a' fails then select the option to find eeprom.bin from floppy.
2) If you do not have a floppy disk drive then from within xboxhdm do the following:
Instead of typing 'lockhd -a' type 'mount /dev/hdc /cdrom'
Next type: mv /cdrom/eeprom/EEPROM.bin /floppy/eeprom.bin
Now when you type lockhd, select the option 'choose another location', and then point it to:
/floppy
This should get you all up and running with your new hard-drive locked and the master password set to XBOXSCENE