...Yep, I'd clean the existing thermal pad gunk using isopropyl alcohol, isoclene or some other thermal interface material cleaner, and apply some thermal compound - it's works better.
Also, every time you remove the heatsink from the CPU, you should clean the thermal interface material from both the CPU and heatsink base, then apply a fresh coat of thermal interface material (whether it be a thermal pad, thermal paste, or thermal compound).
And, about the whole 'frying' issue. How did your motherboard get fried? Was it because of a component on the motherboard (like a capacitor) or was it because the CPU overheated?
Taking into account that the motherboard has been fried to death, I'm guessing the CPU overheated and fried the motherboard. So if the CPU is to blame for frying the mobo to death, then it's unlikely that the CPU itself is in a healthy condition either.
...I suppose you'll find out if the CPU works when you slot it into your new motherboard and test it.
|Desktop PC| |Macbook Air 13" (Mid 2013)|
|Windows 8.1 Pro (x64)| |AMD FX 4100 Black Edition 3.6 GHz @ 4.0 GHz OC| |Arctic Cooling Freezer 13 PRO| |Gigabyte Nvidia GeForce GTX 560 Super Overclock 1GB| |ASUS M5A78L-M/USB3 Motherboard| |Samsung 840 Pro 256GB SSD SATA III HDD| |Kingston HyperX 8GB PC3-14900 DDR3-1866| |OCZ ModXStream Pro 700W Modular PSU| |NZXT Vulcan Micro ATX Case|