Have you pulled the codes lately?? I had a similar situation and the DME was shutting down certain cylinders due to what I think was a CCV/PCV issue. Sucking oil/water into intake. I would look into your CCV system and replace/modify it. I think the tolerances for the combustion were pretty tight and the DME saw there was an issue. By restarting, it resets and starts to monitor again and fires all plugs, etc. Just my 2cents-but that is my experience. BTW, I have modified my CCV to use a PCV and the engine runs perfectly and I am not using any more oil. And, it has 210K miles! Keep us posted.

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Dave S.
Northeast
2003 4.6is
2005 E53 4.4
2003 E39 Msport(a REAL ONE!)
1959 Fiat 600