I just put a motor and automatic trans that has 46,000 miles on it in my sons 2003 kia rio. It runs good and was shifting fine but after a few miles we started loosing overdrive, then drive and when we came to a stop and took off again it wouldn't come out of 2nd. We had trouble with the plug on the newer trans that slips over the rod on top of the trans that connects to your shifter inside. It looks like some sort of sensor switch. It wouldn't stay connected when plugged into the wiring harness and kept the car from cranking and seemed to affect the shifting. We switched it with a used one and worked fine at first but then went back to the shifting problem. Does it sound like a tranny problem or is this piece we switched a sensor that affects when the gears change and needs to be replaced with a new one. The guy we got the motor and trans from is pretty trust worthy and will switch the trans out if its a problem.
