Help restoring disk and booting from external clone

Yesterday I tried to boot from my external clone just to see if it was possible for me to do it. After going into sys prefs and clicking boot from clone restart, as the computer was restarting up it froze or couldnt complete the restart so i simply hit the power button and shut down. I then turned the computer back on and the computer booted from the internal hd but after start up ALL my apps that started with the letter a-i were deleted. luckily i had a clone to simply copy and paste the missing apps but i wanted to do a disk restore but the disk utility would not let me choose a destination. I also tried doing a disk restore using intego personal backup which also i had problems with doing. Could someone please give me help with restoring my disk? And also explain why all the apps were deleted?

Butlins,
Welcome to the Apple Discussions!
The fixed 640x480 display resolution indicates that your external drive is missing the drivers for the eMac's video hardware. You can build the OS on the drive using the OS X install disc that came with the eMac, but that's a model-specific (gray label) disc that only has a full set of drivers for that particular Mac model. You really want to build the external drive's OS using a retail (black label) OS X Install disc that was released at or after the same time as the most recent Mac you need to be able to boot; retail OS X Install discs (should!) have the necessary drivers for all compatible Mac models released prior to that particular OS X disk.

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