To upgrade the HD you need to clone the HD with a good 'cloner' I had success with "PC INSPECTOR clone maxx" it runs Linux also.
I used http://www.ultimatebootcd.com/
it has lots of trendy things on this CD, I used the "PC INSPECTOR clone maxx" to clone the 80gb to my 500gb HD.
NOTE: I originally used ghost and other programs using sector copy & tried file copy but they caused errors when the MK4 booted. (PC inspector clone maxx worked)
So the next thing is to enlarge the partition.
I used a handy tool on the CD called "Parted Magic" this was excellent as it was linux to start with and would preserve various things, and the BEST part is it's all GUI so no stuffing around with random linux commands. With Parted Magic, you need to select the partition group first and expand that into the 'unused space' then you can expand the '/home' or /dev/hda9' into the unused space.
After 3 minutes and 20 seconds the /home was expanded!
I then installed my new drive into the MK4 box and all booted perfect, it booted faster and quieter, also the seek between tracks and recording and loading the radio was much faster.