I just installed a D5 pump and when at full speed it runs at around 4800 rpm and is really quite noisy, with all the fans being silent.
Compared to your pump though, mine has a whiny noise. Yours sounds heavy, like it is resonating the whole case.
The previous pump was a cheap Chinese one, but despite running at around 4000 RPM, I could not hear it! This D5 pump is connected with a PWM connector, so now it's running in between 2500 and 3200 RPM. I can still hear it spinning up every now and then, which is just annoying.
For such an expensive pump that seems to receive allround praise for performance, I am honestly a bit disappointed that it is beat by a cheap Chinese pump in terms of silence! Really weird.
I do have it mounted with double rubber mounts. One set of mounts holding it to the spacer plate and one set of rubber mounts holding it to the chassis. I haven't tried playing a game with this pump connected yet, because I literally just installed it (I did let all the air get through first), but if it gets noisy while playing games, I think I will just put the old Chinese pump back in place, however silly that might seem. =/
Anyway, how is your PC doing now? Still a bit on the noisy side, or did you manage to silence it somewhat?