I am leaning towards just replacing the CPU and see if that will cure the problem. My question is that if it does not cure the problem will I do any harm to the new CPU and then can I use it in a new compatible motherboard?
mate, a new CPU of that kind is probably going to cost you just as much as a new cpu and motherboard of the current generation, let alone good luck finding an old pentium D. I'd just replace both. It might cost you a bit more, but youll have a new system. That old mother board that "might" just still work, might just be at the point of dying, and then after you buy the new cpu and it works, 2 months later the motherboard dies. just spend the bit extra now, and be safe, no risk.
not to mention, if you buy a new Pentium D, and it does not work...... money gone!
I hope I've made my case