Rear end location wrong? IM STUMPED!!!

Would this include leaving the front spring brackets (4 nuts each) and the rear spring brackets loose as well, or just the bolts that go through the eyes of the springs?
No. Just the front spring bushings and the U bolts. The rear hangers can be tightened to spec, since they swivel pretty freely. Don't forget the final torque spec on the u bolts is only 45 ft lb. I don't know what the front bushing bolt spec is but it's in the service manual.