how do you designate which of two bootable partitions are active?
It looks like both Live Ubuntu and Clonezilla use the grub boot loader so theoretically you should be able to dual boot the flash drive. I could not tell you how to do that.
As to the Ubuntu 10.04 issues...
Recent Linux kernels (all, not just Ubuntu) have power usage issues. Here is a thread which has just started on the issue with links to some details. http://www.linuxquestions.org/questi...ubuntu-923276/
Was to the immediate overheating caused by this - possibly but I would tend to think not.
The no gui issue sounds like an issue with the video driver vs. your video card. Here is a post in the Ubuntu forum to look at. Also follow the links in the post for some good info. http://ubuntuforums.org/showthread.php?t=1475667
If you look here https://wiki.ubuntu.com/X/Bugs/Lucidi8xxFreezes
a few paragraphs down
From the LiveCD:
1) At the purple screen with a keyboard and stickfigure, press Enter to get to the menu.
2) Hit Enter to select your language, and then press F6 and then Esc.
3) Add "i915.modeset=1" after "quiet splash".
4) Press Enter to boot the LiveCD.
Try this and see what happens.
But the important thing is to get the heat issue under control so the machine will run long enough to do some more troubleshooting. Perhaps the heat sink needs to be dusted? I know my desktop PCs tend to accumulate a lot of dust over time and a shot of compressed air results in a cloud of dust and a cooler running machine.