is the HDD fast ?
IDE or SATA?
that can be many things...that "lag", it can be your RAM that got fried due to the heat, it can be your processor that also heats and doesn't cool off enough, etc... :/ mainly overheat i would say...when PC overheats the performance isn't the same.
hard to say clearly what it is without looking at it :/
you can get a free program that indicates the temperatures on your PC, then you see if thats the problem or not.