The best flush I saw online used I believe dish soap. (and lots and lots and lots of water).

He had a trans cooler failure put oil info the coolant so he needed an emulsifier to remove the oil. I think that would work very well to get out any debris without having enough base or acid to be a concern with the aluminum block.

I would refurbish the transfer pipes when changing the water pump. I have photos from when I did chain guides on m62tu. The ends of the pipes were quite corroded so I figured out a way to attach the pipes to a drill and use scotch bright pad to polish there ends to a mirror finish. I also sealed painted the outside to prevent the corrosion coming back.

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2011 E70 • N55 (me)
2012 E70 • N63 (wife)