For those stumbling on this thread a little additional info.

The rewiring solution is found here btw: ***RESOLVED*** 03' UK MCS with HK and Sat Nav, want to get TMC to work? - Page 2 - MINI2 - MINI Forum

Visual comparasion between Alpine and Siemens is found here: Factory MP3 Headunit part numbers - MINI2 - MINI Forum

On a side note I think it may be related to the joining of A5+A6 and pin 9 and pin 15 in this instruction manual http://www.motoringfile.com/howto/CD%20Changer.PDF (page 9 and 10) but havent tried it.

Currently I'm running my Alpine with the MKIV, as a result I have no audio on my cd changer on my right front speaker so basicly not using that. Need to put the MKIII back in to see if I didnt damage anything with trying different wire combos and then work forward from there again

This issue seems to be related to older R53 models with navigation, CD changer and H/K for newer R53's its drop in and play.