While your doing repairs and your still having #3 misfire, it can be frustrating, but its not a bad thing (because all the repairs your doing had to be done anyway).

Over the last bunch of years I've captured many of the e60 misfire issues and their solutions. I've put the issues into a file and here's what it looks like (below). I provide the data to you so we don't rule anything out that could be obvious. I did mentioned a few of these earlier.


- your new coil pack on #3 is faulty or DOA
- your new spark plug on #3 is faulty or DOAo The internal mechanism inside the oil filter cap could be bad. The inside could be loose that holds the oil filter. People have mentioned when this is absent or loose it causes idle problems and misfires

o Look at spark plugs for oil in the bottom well on the plug

o Look at the plug. Is it wet with fuel? If so you have a leaking injector and it needs to be replaced

o O2 sensors can cause a misfire. 02 sensors have 100,000 miles, old, faulty and covered with oil?

o Vanos solenoids are faulty (replace with OEM)

o CCV cracked or cracked vacuum lines. Replace vacuum lines

o MAF sensor is faulty

o Fuel pump weak

o Valve tronic motor failing

o valve cover leaking

o Eccentric shaft sensor faulty

o Air filter clogged

o Intake rubber boot might be cracked

o Fuel filter is clogged

 

Looks like a solid list

 

N54 doesn't have Valvetronic. Hence no eccentric shaft nor VT motor.

I still say check compression. The diagnostic seems to have covered faulty parts.

 

I have seen a couple of Exx cars that had water intrusion in the DME harness. Pull it and inspect all connections. You can also test for connectivity between the harness ends for cylinder 3.
Another thought is the MOSFET for cyl 3 inside the DME is bad. That is actually somewhat common on N54s.