So I changed my brakes recently and found out my whole brake setup is from a 2007 a4? is this common in 06 A4's built midyear? What other parts may be from an 07?

 

all of them. nothing changed. parts are interchangeable between most b6 (2003-2005.5) and b7 (2005.5 - 2008)) besides the obvious body components ((aside from the door blades)). interior is 99 perfect interchangeable. but for the B7 everything in interchangeable.

 

The brakes are the same from 2006-2008.