Well, SF (SpeedFan) is generic and you haven't configured it to read the proper temp for your CPU and system - it's just backwards. It comes with templates for some popular mobos, others you config manually. Use the temp monitor software that came with your mobo to find out what the actual temps that are associated with what actual devices, then config SF accordingly. It's your CPU or PWM that is probably 50 and your system is probably in the low to mid 30s - duuuh... That CPU is a bit warm for being cooled by a Freezer Pro - but it may just be your SF config. Perhaps you need to re-grease it, tighten up the clamps whatever. But 50 or so is nowhere near the danger zone for modern CPUs. Over 60 deg C, I'd begin to worry a bit.
Your HDD temp should be controlling the fan that's in front of it (the intake fan in your case) - the sensor that's related to that fan should be taped to the top of your warmest HDD (around 35 is plenty safe for the set point for HDDs). The rear case fan should be controlled by a sensor placed in the warmest air temp. within your case (perhaps hung from the top in the air near the top), not on a bridge chip as that would always have your rear fan running too fast. Any other fan that is controlled should be controlled by a sensor that is on or near something related to the fan. That is all common sense.
. I prefer manual controllers - I even have my CPU fan on my Aerogate 3. You apparently have the fan on the Freezer connected to the mobo. If you are allowing the mobo to control the CPU fan speed, you should put that on full speed 24/7 as that fan should be very quiet even at full speed and will drop the temp. Right now your mobo is just allowing it to run fast enough to keep the CPU at a safe temp.
. That's why I use manual control as I prefer my judgment to that of others (or mechanical devices like mobos).
Damn, I probably just killed my chance at a fan sale...

__ Got dust bunnies inside your case and your Freezer fins? Wouldn't you like to try positive pressure, hmmm?
.bh.