Keep us updated as to your progress... I'm interested to hear also.
I had engine malfunction once, but it was only a mis-fire on 2 different cylinders. After a quick fix I was on my way.
The majority of these engines have been extremely reliable, so even if they patch yours up, chances are it will be fine. Obviously your concern is warranted as it's your baby, but you're lucky because you are WARRANTIED and any problems will be fixed free of charge.
You may have to endure some headaches, but here's to hoping you get everything worked out. I'll be looking forward to updates.
My M3 is for sale here