Yes, the later 3.8's with the Nurburgring brakes have unique pads unfortunately - the difference to the earlier 3.8 pads seems to be slight, but enough to screw up any chance of finding a set easily.
I ordered a set of Ferodo DS2500's for my last change only to find they didn't fit. You can get custom pads made to any pattern but it gets very expensive (about £200 a set unless you do a 5+ group buy - ).
Have a word with either Bexley Motorworks on 020 8304 9797, Birds on 01895 810850, or Moseley Motorsport on 01952 503992
If price is of no concern then the best upgrade would be a new AP/StopTech brake kit. You could go to 360mm discs with 4 or 6 pot calipers and a ready supply of AP-compatible pads from Ferodo, Mintex, et al. - £3k is a bit steep though. It may be possible to simply buy similar spec AP calipers to fit the standard BMW discs.
BTW just take a spare set of pads with you - it is only a 10 minute job once you have the wheels off.