Documented pin usage on the Left Hand switch cluster connector
pin 1 (White) High Beam
pin 3 (Blue/Red) LH turn
pin 4 (Yellow) Low Beam
pin 6 (Brown) Ground
pin 7 (White/Yellow) headlight pwr from RH controls
pin 8 (Green/Blue) High Beam Flash pwr
pin 9 (Brown/Yellow) Horn - active low
Documented pin usage on the Right Hand switch cluster connector
pin 1 (Black/Yellow) Start Sw.
pin 2 (Green/Yellow) Kill Sw.
pin 3 (Green/Blue) Light pwr.
pin 4 (White/Yellow) headlight pwr to LH controls
pin 5 (Blue/Yellow) RH Turn
pin 6 (Black/Green) Start Enable
pin 7 (Grey/Blue) Parking lights
pin 8 (Brown) Ground
pin 9 (Green) Kill Sw.
Ducati 999 RH Controls pin mapping
Duc BMWpin 1 -> RH pin 1
pin 2 -> RH pin 6
pin 3 -> RH pin 2
pin 4 -> RH pin 6
pins 5 through 8 are not connected

Ducati Motard LH controls pin mapping (pins are numbered 1 through 10 left to right).
Duc BMWpin 1 -> see Circuit
pin 2 -> see Horn mods
pin 3 -> see Circuit
pin 4 -> RH pin 3
pin 5 -> LH pin 4
pin 6 -> LH pin 1
pin 7 -> +12V switched power
pin 8 -> Ground
pin 9 -> not connected
pin 10 -> not connected
Horn Mods. Normally the BMW horn switch connects to Ground, which completes the circuit on the horn relay and the horn blows. you'll have to rewire the horn relay to ground Pin 85 on the relay (Brown/Yellow) and connect Pin 2 of the Motard switch to Pin 86 of the relay. Make sure to remove the Green/Red wire from Pin 86 on the relay first.
Circuit: To make the turn signals work, you'll have to completely replace the BMW flasher with an aftermarket 3-pin flasher which probably should be LED-compatible for maximum flexibility. One pin of the flasher goes to +12V, the second goes to ground and the third output goes to this circuit. Then you'll have to build the following circuit to make the turn signal switches work properly. Switch S1 is the Motard turn signal switch. LMPs are the existing turn indicator lamps on the bike.

I haven't tested this circuit so I suggest you prototype it first before committing to a production unit. that gets installed into the bike.
How the circuit works: The Motard switches output +12V constantly when signalling either left or right. When the turn signal is signalled left, power is applied to Q1 which pulls the base of Q3 to ground. this turns Q3 on and the flasher output is directed through to the indicator lamps. When the turn signal switch is signalled right, power is applied to Q2 instead, which turns on Q4 and causes the flasher output to be redirected to the other indicator lamps. When the turn signal switch is in the center position, neither circuit is active and the flasher output is cutoff.