Usually the cooler for an auto trans is setup in the return to the pan from the pump/valvebody.
My experience has shown that the OEM's use a counter-flow arrangement (this has not been tested on a metro). ATF flows the opposite direction of the coolant. A study of heat exchanges will show you that this type of heat exhanger will give a better cooling capacity than fluids flowing the same direction, so this makes sense.
An easy way to check this would be to see which line is hotter after a drive, the difference may not be much.
It's not likely that the earlier transmissions are a direct swap, by 2001 most automatic transmissions had electronic controls. Earlier models may or may not have had this, but the electronic controls they have will most likely be different.
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