Looked into this in more detail today:
Tried changing the ground location - no luck.
Tried moving the input signal wires away from some of the cables in the boot - no luck.
I was not sure if the problem (whistling noise which rises and falls with revs and electric water pump interference) was a result of the inputs or the power to the amp.
So I took my i-pod outside with a 3.5mm to RCA jack and plugged this into the amp for the input signal. Started the engine and the noise is then completely gone - so the issue is interference on the input wires. Strangely the interference is on L and R because I tried unplugging them one at a time but the interference noise is still there.
The input wires are running to the BMW connector on the left hand and right hand sill of the car.
Tomorrow I am going to change these to shielded RCA cables.
I plan to move the vibe speaker to RCA convertor to the sill and from here connect the RCA and run back to the amp with shielded RCA cables.
I bought two RCA splitters today so I can then split into the FRONT and REAR channels of the amp.
Will report back tomorrow, but for anyone doing this, it is probably worth running RCA cables for the signal input to the amp as the poster above has done.
I will post back tomorrow with the results.