|You got an overclocker's heat sink but you also got the i5-2400 which is not overclockable??? If you wanted to overclock you needed the i5-2500K; If you were not then you did not need a massive heat sink (unless tropical temperatures without A/C).|
You did not mention your hard drive make and model. The typical front panel LED that periodically flashes is your HD indicator meaning a program is accessing your hard drive. If you purchased a slower hard drive or one with a lower cache then that is possibly your bottleneck and is causing your problem. Your board has the ability to use SATAIII at 6BG/s so if you have only a SATAII 3GB/s drive, especially if it has less than 32MB cache you could be causing the slow down right there.
Do not overlook heat problems, especially if you have not built many computers. Too much thermal compound is nearly as bad as too little since it limits the heat transfer. The more complex heat sink hold downs that come with the heavier heat sinks must be torqued down evenly as well as firmly, too much pressure on one side and you get poor heat transfer over most of the CPU's surface. Install SpeedFan or similar program to monitor your internal temperatures while running programs to give you some clues as to where the problem is. If you are running even a little bit hot with that set up, look for the problem, but I would completely redo the heatsink mounting with fresh thermal compound on freshly cleaned surfaces.
You have to be a little bit crazy to keep you from going insane.