Ever since a year ago ive had a mild herniated disc. on and off it causes lower back pain especially when waking up. why does it feel like my whole lower body cracks and feels almost like it is breaking and popping when i wake up and stand?

An injury to lumbar disc causes a shortening of the spinal column. Continued attention to your posture, morning stretching, abdominal strengthening, and avoidance of twisting during lifting should be a part of your life going forward. The cracking sound is tightness based. Review your physical therapy exercises. Be well through self care, and get checked if you're feeling weak or numb.