Make sure the machine is physically disconnected from the mains. Find the BIOS (cmos) clear jumper and clear the BIOS.
Now see if it will boot.
939 CPU's should have the whole of the surface in contact with a thermal solution as they generate a lot of heat. The whole idea of the thermal solution, is not to stop the CPU coming into contact with the heat-sink, but to transfer heat from one to the other. Therefore, your small patches would NOT be suitable.