I went to change the rear brake pads yesterday.  Pulled the old ones out but couldn't get the inner one back in but you could throw the outer one in from across the room. After the odd swear word I realised that the calliper is not even close to being centred on the disc.

Well it's been through a few tyre changes beages so the possibility is there that someone mixed up spacers at some point, it's not frozen on the pins is it?  That's something that does happen quite often.

I used a set of drills as feeler gauges and there's  roughly a 3.5 mm difference either side. The inner pad that came out was nearly down to the metal and the outer pad was maybe 10% worn.

I am thinking that's the only way it could happen. 

If your sure the caliper is ok maybe the spacers are on the wrong sides? They are different but off the top off my head I can't recall how.

43654-00A disc side

Yeah mate, there's a big difference either side. The one on the left looks like it's well over an inch long and the one on the right is around 1/2 inch. When I pull it apart tomorrow I will know more but I'm thinking I might have to adjust the spacers to move it over about 2mm.