It may be a good idea to fit your case with some casefans to lower the temperature. If your case has a good airflow, the temperature will drop considerably. I had an Athlon 1400 (AMD's ultimate hothead) running at 1600Mhz in a case without any airflow... just the fan of the CPU, no casefans. Although it wasn't unstable, I had a case temp of about 70C. Not that good! So I added just 2 casefans and it dropped about 25C. Way better. It's not just the CPU that suffers from high temperatures, but the other components as well. Especially the harddrives, as they tend to die a lot earlier in bad ventilated cases.
About the programs without serial numbers: of course I do not know what programs you are running, but it might well be that:
1. Older programs can be replaced by better and newer programs that might be totally free of charge (freeware, open source etc)
2. I guess that most companies have a database of registered customers. Why not contact them and ask for a new serial?
And at last, about the reinstalling etc. If you exchange parts (especially major parts like the mainboard) reinstalling is a very wise thing to do, if not required. This goes for both the AMD and the Intel platform. Why switch to Intel btw? Intel's more recent CPUs produce more heat than modern AMD CPUs.
My advice: get some casefans (you really should place 1 or more intake fans in the front of your case and maybe one more outtake fan in the sidepanel) and maybe a better hs/fan combo for your CPU. Make sure you use thermal grease (not too much, as this will reduce the cooling performance).
And if you want to silent your system, better look into slowing down your fans. Get either a fan controller or put them on 7V (by using the +5V and the +12V, in stead of the 0V and +12V).
My case is equipped with 13 fans and it produces less noise than quite some system with just 3 fans. It's all a matter of tuning :).