Download load and burn an Ubuntu CD and boot from it. Then try before you install
. Once booted in do back to download mode on the phone and plug it in and you should see all the partitions. From there you should be able to copy in the stock files. Never tried this before by copying the ROM and such. It should work, the only thing to be concerned about it permissions to files. Also make sure that before you boot into Ubuntu that you have the stock ROM extracted into a folder on your C:\ of your Windows computer. You should be able to access it through Ubuntu in read only mode.