This sounds similar to an issue I had with mine when I first got it.
Threw the same codes and also tried a lot of the same diagnosis - removing injector plugs etc.
You need to do a balance test on the engine and a back flow test on the injectors. I would say that could be where your problem is - a blocked injector. Sometimes they get carbon build up and at low pressure they can't atomise the fuel properly - it sort of just dribbles out and you get rough running. It's worth getting it diagnosed with these tests before you go ripping the manifold off and replacing things. If they do diagnose an injector, don't let them convince you to just scrub it off with a wire brush - it's asking for trouble.
Have a read of my thread here:
http://www.xoutpost.com/showthread.php?t=98737
Don't be too concerned about the glow plug code. Lots of BMW diesels with a few kms on then will throw this code, but as you said, if you're not having trouble starting it cold then it's probably not a major concern.
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2005 3.0d Sport - Sapphire Black
Engine : Bluefin Superchip Tune,
Wheels & Sus: Style 168s (10.5s all round), H&R RDA Spacers, Bilstein B12, Eibach 40mm drop, Whiteline RSB
Exterior: Le Mans flares, 4.6is kit F&R
Interior: Dynavin N6, Blackvue DR650 dash cams
My Build Thread: http://www.xoutpost.com/bmw-sav-foru...run-sheet.html