You mentioned that when you had the tranny flushed, the fluid was "Black". I would not think that this was the fluid as much as it was "clutch dung" commonally found in an ATX.
Since you still seem to have a cooling issue, I would have to think that you might be having some issues with the internal cooler found in the radiator. It is not overly uncommon to have problems with this area. I have read somewhere that it should actually be flushed seperatly from the rest of the unit along with the cooling lines because of the amount of clutch particles that can build up in these areas.
Whoever had the car prior to you, did not take very good care of the tranny at all. It would not be a bad idea to go ahead and have an external cooler installed to resolve the cooing issues, because we all know that heat will kill an ATX in a heart beat. It is a good thing that you put the trans fix in there also. It is also not uncommon around here for someone to have their tranny flushed (one like yours that the fluid was not changed on a regular basis), which breaks free all that black stuff that you saw, to only be followed a few months down the road with line pressure issues. The trans fix will help with keeping that under some control.
