If you are now able to boot to the GUI desktop, you should be able to access the external drive with no trouble. Getting to the data on the Windows drive can be a little more trouble, since Windows could have messed up the filesystem on that internal drive. I suggest booting the CD, starting the file manager, and then clicking the drive icon for the internal drive.

If you see the folders for the Windows partition, go ahead and plug in the new drive, click its' icon when it shows up, and then proceed to drag-and-drop some useful files to the new drive. Once you've backed up the goodies (My Documents, email, etc.) you can then try your hand at repairing the broken Windows stuff. If it's too big a job, I'd say at that point that it's time to use a (blow the data away) Windows "rescue" disk or boot-option.

Cheers!
Krishna