more case fans are not necessarily the answer. You need to make sure you are creating an effective flow of air through your case. There are two basic ways to design your airflow. One is a positive pressure system where you pump lots of cool air in to the case, to cool it down. The other is a negative pressure system, where the emphasis is on removing the hot air. Most individuals build positive pressure systems, but cases professionally designed tend to use a negative pressure system. That's not to say that one is better than the other per se, but the latter is certainly cheaper in non-critical situations. Make sure when you design your airflow, to make it so that air is consistently replaced throughout the case, especially in critical areas (CPU, GPU, HD's).

however, it's not obvious that heat is your problem. Case/CPU temperatures tend to even themselves out long before 12 hours of consistent use. Not to say heat isn't your problem, but you might want to look for loose connections that might be corrupting data slowly over time or other small things like that. good luck.