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Make a mirror image using <<macrium reflect>>(free) onto a new disk - I've done this with mine and afterwards, you can just take the old disk out and run with the new one. It even does the boot sector which means there's no installation needed. Do delete all the crap and defrag it first, it'll make it a bit snappier later.
One thing to check and I know this sounds silly, take the fan off the processor and clean the fins on the heat sink. This is often overlooked and can cause the symptoms you note.
The chip gets quite hot when starting up and slows down if it can't get enough cooling - after startup, the amount of work you're doing on the thing isn't enough to stress the chip and it doesn't get hot.
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