Another thing to check since you tightened up the bolts while on jack stands are the rear leaf shackles. Looking at the car from the side, the shackles must be angled to the rear of the car. If they are pointing straight down or forward they will not operate properly and would keep the car sitting high in the rear.
Also, since bolts were tightened while on jack stands; after loosening the bolts to let it settle you will probably have to jounce it on each corner a bit to make sure it settles to where it should be. Did you also tighten the front end suspension while on jack stands? If you did - you will need to do the same up front.
