How about the pump and hard drive? Do you think they could be part of the problem? Some people try to soft mount their pumps in order to cut down on noise. The same goes for the hard drive. Most of the Lian Li cases I`ve used were somewhat prone to increased vibrational noise and rubber grommets do little to help. Mounting the drive/pump on a piece of open cell foam should be much more effective. Overall, I think that isolating the sources of vibration from the rest of the case should be the most efficient way reduce vibrational noise.
I like your idea of push-pull fans. The hard drives are mounted by the bungee cord suspension method, and there are 4 of them now. They are all sandwiched in the front hard drive cage, the one with the single drive in it in the photo. The bungees made a big difference in the transmission of vibration and noise to the case, they effectively eliminate it. They are cooled by an Akasa Apache that is mounted on very thin rubber pads (front intake fan). Since the drives are mounted so close together, I built a little air-flow duct that funnels all of the fan's output directly to the drives and keeps it from going around them. It is made of 5mm neoprene.
The pump is mounted on the removable motherboard tray, but it is isolated at least a bit. I used a block of this stuff, Petra's Gel Stuff
between the pump and the motherboard tray. Since the pump is mounted on the motherboard tray, it is on a vertical surface. To hold it in place I used two long nylon screws and nylon nuts. I figure that the nylon, which has some give to it, will transmit less vibration than steel screws would. Further, the pump is mounted very loose, so it can essentially "ride" gently on the Gel Stuff and is not tightly coupled, by the screws, to the motherboard tray. You can push the pump around a bit very easily. After mounting it this way there was a vast and dramatic improvement over the little neoprene pad that the pump came with. I am toying with the idea of making an L-shaped mounting bracket for the pump, so that the screws don't need to hold it up, just keep it from wandering away. That way the screws will be much looser, and transmit even less vibration. The bracket would also free up some space at the front of the motherboard tray possibly giving me the room to mount the Aquaero controller on the tray as well, and keep the whole water cooling system on the removable motherboard tray.
Your idea for push-pull is brilliant. I might just do that, and eliminate the top fan. But there are two problems to overcome. The first is figuring out how to mount the fan that will be next to the case. The best that seems available is the little silicone fan isolators, the ones that are 120mm x 120mm, and supposedly keep the fan isolated from the case. They are really to thin to work. There is one between the rear fan and the case now. I will want to figure out a much better mount for the fans.
The second problem I may be able to live with. With only the radiator outside of the case at this point, the case is 58.5 cm deep, front to back. It is way too deep to put on any shelf as is, but will gain 5 cm more in depth with two fans out there as well (not counting isolation/soft mounting). I don't want to put it on the floor, as it is already deeper than my desk. I also want the dvd drives easy to reach. And I have Great Danes who sometimes get quite playful and energetic, and the frequently shed a lot. There is thus lots of dust and fur in the house. One of the dogs likes to hide under my desk. Well, at least as much of himself as he can fit under there
Sorry for the long post, but was kind of brainstorming with you guys. But the pain killers are now kicking in and I'm loosing ability to think clearly, so thanks for your responses, have a good night.