Transmission being new...
- the casing is aluminum/magnesium (whatever it is it won't EVER rust)
- Judging the contents of a box by how clean the box is itself doesn't make sense whatsoever...a transmission isn't any different

-black crap all over it = undercoating (won't effect the inside of the transmission)
Of course your engine is JDM. It's the same engine they used in Japan (4AGE), only with an AFM instead of map-sensored setup. There is no difference between the engines used here and in Japan aside from that (as far as I know). Unless it's special in some way, there would be no point to import an engine from Japan, and convert it to the AFM setup
Migs