Ok, I've got round to plugging the original PCM2 back in. Checked the audio settings and they were set to flat :-(
I bought the connection kit from Autoleads, I was recommended their Audi Bose harness which comes with the Autoleads H2L, a high level to low level converter.
Bear with me here, this gets complicated.
1) I disconnected the audio leads (phono) from H2L, music kept playing. I followed the cable to the connector which connects to the car's harness. There is nothing there on the car side.
2) the balance and fader controls don't make any difference via the amplifier, I've checked the HU via the line out, it all works from there and sounds quite good.
3) The active aerial converter has a blue lead, which wasn't connected to anything.
I've come to the conclusion I've been sold the wrong harness and the person who fitted it doesn't have a 100% grasp of how it works. I've connected the blue cable to the power antenna lead on the HU, not suprisingly, the radio reception is much better now.
My PCM2 & Bose system definitely doesn't have the MOST system.
Next steps is to contact Autoleads and see what can be done. Hopefully I can move a few of the pins and wire it up from the pre-out, low-level output and regain balance, fader and improve the sounds quality.