Based on what you mention I am not so sure I would be too quick to replace the HSF for the CPU.
I've noticed that, mainly when transcoding video to watch on an XBOX 360, the CPU fan ramps up. If I don't adjust the other fans, the CPU fan ramps up to 100%.
(I have recently disassembled the rig, cleaned it out, installed filters, cleaned and re-applied thermal paste and reseated the sink.)
That tells me when doing CPU intensive task the CPU gets hot which is to be expected. Then the CPU fan speed ramps up which says that is doing as expected. The problem I see is that the heat being removed from the CPU isn't able to exit the case as easily as it should. When you manually ramp up those case fans and get the heat out of the box then things work as they should.
Fans are relatively inexpensive as would be a front panel fan speed controller kit. I might think about replacing those 3 speed internal fans. Personally I have several around here I yanked out of systems.
As to using the CPU header to control other fans? That can be done but you would have to add a small home brew circuit. A 3 wire (or 4 wire for that matter) fan header uses PWM (Pulse Width Modulation) to control the CPU fan speed. You could use that PWM signal to drive maybe a MOSFET and let the added MOSFET hack the load of additional fans. Power the circuit with 12 Volts off the PSU that isn't used. When the CPU ramps up in speed all the fans slaved to it would ramp up in speed.
Overall I think the problem is when the CPU HSF does its job the hot air isn't being moved out of the box enough. Hot air in the box would also contribute to the CPU heating up quicker.
Just My Take