Damn Dude you got Buzzard Luck........ I am sure you checked the fluids first.
The top rattle could be from the shifter coming loose, basically becoming unbolted.
The bottom clicking/rattle could actually be a broken gear/clutch inside the tranny that is hitting when it rotates. You could pull the pan and see if you can see any material in it. But I seem to remember years ago something similar happening to an auto and the problem was internal.
You may want to talk with some local transmission shops to see if they have had an issues with this type of transmission in the past, just to give you an idea.
MUSTANG...Like Bringing a Hot Dog to a Steak Dinner....There is no comparison.