I have chased crap brakes on my E36 for years and have tried everything to get air out of the system. You may have to bench bleed the master if it was run dry. The BMW procedure as per DIS is to pressure bleed the system, disconnect the pressure, run the bleed routine while pumping the pedal for each corner. Pressure bleed again, then no pressure bleeding once again. If you have the software it should walk you through it. I think this works to get small bubbles out. To try and evacuate an entire system or length of air, you may have your work cut out for you.

When I bleed (the track car), I switch fluid fluid colours so I can see it come out. If you are certain the fluid is flushed, then the air is in the master, ABS unit or the pump circuit. You may find that cracking the fittings at various points throughout will help bleed the air out in those sections. Always keep the pressure bleeder on and full when your doing this to avoid making it worse.

I haven't got into these brakes yet, so my experiences are only from years of messing with my E36 brakes, so take it with a grain of salt.

__________________
Daily Drivers:
- 2008 535i, 320,000km
- 2004 X5 4.4, 01/2004 production, 420,000km
- 1997 328i, 350,000km

Track:
- 1996 328i, track/race car, ~300,000km

Winter:
- 2013 Ski-Doo MXZ X 800 E-TEC, trail can
- 2007 Ski-Doo MXZ Blizzard 800 HO
- 2001 Ski-Doo MXZ 600 w/800 engine, exhaust
- 1978 Ski-Doo Olympique 340 (vintage race sled)
- 1977 Ski-Doo Olympique 340E