Well I know Tammzy has never used the Z9 case, so i'll offer some more hands on experience. I have recently installed a Bitfenix 5 channel fan controller and added two 140mm Bitfenix spectre pro fans to do an end user review. I'm still writing up my thoughts and need to upload the pics etc but I can share my thoughts quickly with you now
On the stock fan setup my 555BE @4Ghz on a gelid tranquillo heatsink, peaked at 45 deg. With 5 fans (3 120mm zalman LED, 2 140mm bitfenix LED), I set all of the fans to minimum on the fan controller and got the same temps with the rig being a lot quieter.
If I set the sliders to max it knocked 5/6 deg off the max temp under the same benchmarking. I also noticed that the GPU ran cooler, no doubt because there was now a fan at the bottom of the case pulling in cool air.
Is this only "marginal" improvement? I guess that depends on the individual. The zalman fans aren't bad and have a good bright LED. The Bitfenix fans are better and shift more air, I'm able to turn off their LEDs via the fan controller too which is a nice touch.....so yes I am tempted to replace the remaining Zalman fans.
Your setup is different though. I always suggest a modular PSU in midi towers, you sadly don't have one so you will no doubt have a mess of cables hidden at the front of the case in the HDD bay. These cables are blocking airflow which isn't great
Before you start spending money, see what temps you get and how far you can push your CPU on the stock setup. If you are not happy with the temps, I would suggest adding two 4pin (PWM) fans to your matterhorn heatsink (I can only mount one fan on my gelid heatsink) and move the old heatsink fan to the bottom of the case if you can, to get more air in the case.
If noise bothers you then you can cut the hexagonal mesh out that covers the fans. It doesnt cost you anything but time and it definately improves airflow and decreases fan noise. If you want to add a fan controller at some point that's cool it's a nice addition but your first port of call should be to maximise the cooling on the heatsink itself.