Check the trans oil level and see if its full. Take a sample and see if the fluid is metallic looking, if it is, the transmission is toast. The fluid should be bright red and full.
If the engine is running and the car is not moving, only the input shaft, (planetary gears, generator/starter shaft) and oil pump are spinning. When I had mine apart to replace the transfer gear according to the Ford TSB last year, I didn't go the extra step of checking the oil pump drive gear. Wish I had checked it, but didn't know that was another issue at the time. There's some utube videos of the aluminum gear teeth stripping. I didn't see any metal in the oil at the time, so I hope its still ok.
If yours is already making noise, its likely too late. Once metal is circulating through the system its impossible to clean it out properly, as metal gets into the coils.
Its possible when the transmission was replaced, the cooler was not replaced or flushed out, as metal and contaminated fluid will be inside and will work its way into the new transmission
With the amount of trans failures reported here and elsewhere, I have suggested changing the fluid every 1 or 2 years. Its only about 5 quarts so its not that expensive. The Ford spec of a fluid change is 150,000 miles is way too long in my opinion. Although they say to the check the fluid level once a year or 10,000 miles, I don't know if anyone ever does it.