Thanks for your helpful responses!
I temporarily disconnected the 2 case fans and started the computer with only the Coolermaster fan running. It was still extremely noisy, so yup, the Coolermaster was the problem.
I tried speedfan, and was able to decrease the CPU fan speed. The volume is now reasonable. (fyi, it reports the CPU temp to be about 37C at this speed, which seems acceptable)
One more thing though. When I restart the computer, the fan starts up at 100% again (vacuum cleaner speed). I have to use speedfan to manually decrease the speed. My motherboard is ECS (aka "Elite") 915G-M. Do you know how to automatically control the fan speed based on the CPU temp? I can't find any option in speedfan or in the BIOS. I tried installing Motherboard Monitor 5 also, but it doesn't seem to support my motherboard.
Well at least you got it to lower while you're using windows. If you really want the fan to stay low all the time and your motherboard accepts it, plug the fan into a 3 pin connector on the motherboard instead of the PWM CPU fan pin. (I don't know if that makes sense to you but its basically plugging in the 4 pin from the coolermaster fan into say the system/chassis 3 pin on the motherboard. You don't really need the blue wire, which is the 4th pin, its for PWM functions) If your motherboard boots up fine and shows no CPU fan error then you're good to go. (If it does you could probably display the error in the BIOS again). The only thing though is that the fan speed will stay at 1500rpms which when I used to use it was actually decent (around 35-37C for me). I guess you could use speedfan to speed it up when you feel like it but I really have no experience from that point on. LOOK AT SOLUTION BELOW IF WIRE DOESNT REACH.
After looking at a pic of your motherboard it looks like its too far to reach the chassis pins on the motherboard but here's another solution for you:
Disable the blue cable of the hyper 48 fan by removing it from the plug (use a small screwdriver to push it out). So I mean the 4-pin plug of the Hyper 48. Unplug the blue cable , then plug in the now 3- pin cable to the cpu fan connector of the motherboard and everything should works fine. This shoudln't give you a no CPU fan error. As for the speed changing, you can try speedfan for that. Hope that helps.