When BMW produced the facelifted version of the E53, they also made some changes under the bonnet. The pictures below may help those with the later version as the engine cover is different.
1. Wide shot of the facelifted bay as seen when you open the bonnet:
2. Bolts to remove the front portion of the engine cover (Yellow) and the two nuts to remove to allow the removal of the micro-filter assembly (see earlier thread instructions on this)
3. View now you have removed the font engine cover
4. Once you have removed the microfilter assembly, then you can remove the rear cover bolts (Yellow)
WARNING These are NOT captive so you may lose them if you're not careful!! The yellow arrow indicates where the two 10mm bolts are under the wiper motor - you will need to get these out and space is tight.
5. To get at the breather bolts (Red) you will need to remove these three (yellow) bolts that hold the wiring harness in place.
If you are going on to do the air filter (worth it as you have got this far), then you need to remove these bolts (yellow) including the one pointed to by the arrow but which is hidden and partly obstructed by the magenta area. I strongly recommend you get this piece out too as it will make life MUCH easier, and also shift the washer bottle (2 10mm plastic nuts) over a bit to give you room. I didn't need to remove the bottle and did not have the tools to get the plastic shield around the wiper motor out of the way!!
I hope these are of some use.....