I have noticed this as well. The left is a bit higher and the end of the pipe is more horizontal whereas the right pipe end points slightly downwards. Maybe a bit of adjusting by loosening the two clamps on this pipe by the spare tire and twisting the pipes to can get them to be pretty much the same. Also try adjusting (bending) the hanger bracket on the pipe to lower it slightly. If you do it yourself, remove the spare tire to make the job so much easier. I will be trying to fix mine this weekend and will post my results here.
As for the vehicle sitting level. I have noticed that especially with a full tank of gas, the vehicle leans slightly to the left (looking from the rear) The gas tank is along the left side of the vehicl in fromthe the left rear wheel, leading me to believe that with a full tank the c of g has moved to the left. I don't think much can done done here except alway drive on empty (not a good plan) or ensure you carry two heavy passengers on the right side of the vehicle.
03 V6 4Runner Limited, Silver
Borla Exhaust
Nifty Catchall Extreme Floormats