All you need to do now to get those files off the Mac and onto the external is to use Ubuntu's command line (dont get scared, its pretty simple.
Fisrtly create a folder called backups on the external disk, this makes the copying process easier.
Boot up into the Ubuntu live CD as before with the external disk also attached. Bring up two windows in Ubuntu - one showing the User folder on the mac, the other showing the external disk
In the
Applications menu, select Accessories > Terminal
In the command line type
sudo cp -r - this basically sets a a copy command that gives you all privileges, so that your own permissions on the folders are beefed up to all access.
Next use drag and drop to drop the
copy from folder and the
copy to folder from the windows you brought up into the command line - this saves you having to work out the command line locations of the two folders.
Press return and wait patiently for the command to do its work, it will create a new command prompt when done.
Repeat to copy the new folders, or just copy the whole user folder, its up to you.
Here a handy picture to show how its all done.