All these mentions of cooling system components, but no mention of hoses. Inspect/change all coolant hoses, particularly if they are soft. And particularly if you are changing pumps and coolant expansion tanks anyway.

What does the oil separator/crankcase ventilation system look like on a 2004 model? If it is like other engine models, I would clean it out, and replace those hoses as well.

And flush the brake fluid.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue