M54 rough idle and misfiring - with diagnostics

[Siddy1200]

Hi all,

My '04 E53 M54 started to have a very rough idle and misfire one cold morning.

I found the intake boot had the standard splitting issue. Same issue as my e46.

Replaced the intake boot, but that only improved the issue, still have a slight misfire.

I tired my Bluetooth OBD2 scanner, it connects to ecu but won't read codes. Strange since it works fine on my e46.

So I took the car to a auto shop and they diagnosed it for me.
I uploaded the diagnostic pdf, you can download it from my google drive:
https://drive.google.com/file/d/1Oj1...w?usp=drivesdk
Some of the codes are old codes, eg transmission in limp mode. It's not in limp mode now, but it was before.

The report says, misfire cylinder 1,2,3,4,5 (not 6). And ignition cylinder 2 and 5. MAF and DISA.

I have:
changed the spark plugs (they were original, figured it was time for new ones)
Cleaned the MAF
Inspected the disa, flap holds vacuum fine and I can see it opening and closing when I turn the car on, so seems ok but maybe it has a vacuum leak?
Checked the intake pipes for vacuum leaks