Did you say that the H50 fan is blowing into the case?
If it is, then the heat exchanger is cooling your CPU only to heat the case back up.
Make sure the H50 is exhausting air out of the case.
Also when you added the extra 120mm fan to the side of the HDD bays, did you consider what the flow rates were? The red LED lit fan looks a lot larger, and even if it rotates slower it will move a greater volume of air than the smaller fan you have, so the smaller fan will be inhibiting the overall air flow.
Can you move the HDD's into the spare 5.25 inch bays using some cheap adapters? They seem to be blocking 30% of the airflow plus warming the air from the front intake fan.
Maybe remove the blank PCI slot covers, this will allow a great deal more air to move in the case.
Last thing, how warm is your room? Is it near a radiator? Maybe a stupid thing to ask but worth asking nonetheless.
Let me know how you get on as this is an interesting question