It is not uncommon for transmission fluid to become dark in color and develop a burnt smell. More routine service of the transmission can help prevent this. It this point you can do a couple of things. Removing the trans pan and replacing the filter and refilling the trans would be the minimum. Unfortunately unless there is a drain plug in the torque converter this does not get all of the old fluid out of the transmission. In order to do that you will need to have a complete fluid exchange done after the filter has been replaced. Whatever you decide to do I would not recommend to run any kind of transmission flush or cleaning chemical through the transmission. These products and clean to much varnish off of the valves in the valve body and could cause shifting problems to occur after the flush is complete.