You just don't get the D exhaust part, do you? Still think you looking at the ordinary muffler... I suggest you study that PDF, the way the SCR/DEF system works before you start changing things around. You may change your mind after all.
On the tune part, you can remove any of the piggybacks prior to dealer visits and erase any of popped up codes with BMS CANtool or BT cable.
The small rad in the driver wheel well is an auxiliary water radiator. The IC I believe is the second behind or below the tranny cooler, if I remember correctly.
Retired: 2005 N52 E90 330i Sport 6AT
Retired: 2007 N54 E92 335i Sport 6AT
Current: 2012 M57 E70 X5 xDrive35D