Has anyone ever woken up sore in entire body after an ACL reconstruction?

No , not really. Soreness of the whole body after acl surgery is unusal unless you either are having a systemic problem developing concomitanly or you have an allergic intolerance to medication.
Sometimes yes. Body (and muscle)pains are not due to acl repair , may result with any surgery due to muscle relaxants and medications given put the person to sleep , may lost couple of days.It is due to sudden movement of fluids and electrolytes in and body cells, will recover completely.