Many thanks for writing a detailed reply, he did have his multimeter out and was using it but our main concern was the buzzing noise.
I have changed over the RCA phono plugs to plastic ones which I bought from Maplin - I carefully soldered them on to ensure polarities did not touch - back in the car and nope it did not make a difference buzzing noise still there.
Then I swapped the RCA plugs around, into the right channel I plugged the left RCA and vice versa - the buzzing noise went from the passenger side to the drivers side and the passenger side had no buzz
So then my original config was -
Channel 1 - Right front
Channel 2 - Left front
Channel 3 - under seat sub
Channel 4 - under seat sub
So I then
Channel 1 - under seat sub
Channel 2 - under seat sub
Channel 3 - Right front
Channel 4 - Left front
Changed the amp settings/gains to reflect the change and the buzzing still came from the passenger side.
This leads me to think something is wrong from the harness/HU end but as I got back late and did the above in the dark (5pm) with a flashlight I will have to pull out the HU again tommorow and check connections behind.
Also I have noticed when I have the volume on low I do suffer form alternator whine coming through speakers is this the norm?