Great pictures - with some of the errors, try moving the steering wheel all the way to the right, then all the way to the left. That should help clear the BRAKE and 4x4 errors.
Don't ever run the car without the modules - not a good idea

Always disconnect the battery anytime you unplug any module.
That 4.6is is awesome - loved the E53, still have mine, 53k on her now. I only have a 4.4i but I love those naturally aspirated motors, the E53 just feels very connected to the road.
Great mods BTW - and great pictures.
Chris