First try a transmission reset, plenty of info how to do it, now that your battery is okay. Next having done this when you say the car is clunking into gear, is it is doing hard shunts when you go down through the gears particularly at low speed around 3-2-1 gears???? Or when you have slowed down and then you accelerate forward it slams into gear????
Always said I would go back to a 6 series