Sorry for the late replies, I've been trying out your suggestions. None of which have worked, however it really does sound like there's an air bubble in there that would never go away despite how long or what position it's in.
There's a 1/8 foam padding in between the water block and the surface contact.
I'll provide a photo of the pump when I get the chance.
In the end I might just replace the pump as I've seen everywhere on the internet that this pump is supposed to be near silent.