to answer each in order...
No the alignment tools I made myself, but I have 100% confidence in their accuracy. All that is required for camshafts is that the flat profiles at the end be perpendicular to upper head face, when No.1 is at TDC. There is a sensor wheel alignment tool also, but I marked those prior to removal.
I should add this fault existed before the timing failure, the customer had lived with it for 10months, add to that the fact it runs pefectly when cold, and I am happy to rule out any error on my part with timing/building back up.
I can't command a relearn via serial. I have spoken to hickleys on that very subject and they said neither Bavarian technic nor KTS would be able to do it either. Only way to command a relearn without ISTA or some "hexscanner" thingywotsit is to manually move eccentric shaft from the postion it normally comes to rest in when engine is shut down. A relearn has taken place, under command of ECU - this I know for sure, as the fault code has dissapeared and I could see the shaft had moved afterward.
Using a texa navigator txt, which to be frank is not a cheap tool, it is sometimes lacking in areas though (as they all are - except dealer) I have been trying to get hold of ISTA/D as I could run it in Pass-thru mode using the TXT, which would give dealer level on BMW - however getting a download of ISTA is easier said than done.
So I've got lean in cylinders, and lean on one o2 sensor - which is in open loop, LTFT's showing approx +8% on fuelling - which backs up the lean trend, and a second o2 sensor showing fairly normal operation.
What a mess.
EDIT: What do you make of that dwell time on cyl3?
Further EDIT: I have read that throttle is normally sat fully open, with valvetronic doing all the metering of air under normal conditions, meaning manifold would rarely be under vacuum, seems to ring true, as they have a camshaft driven vacuum pump for servo.