bashful

I have a 95 Explorer and it runs fine as we're driving...but when we come to a stop the car will shake and on rpm showing when car is idle, will fall below the 1 and then it kicks back up. It doesn't do it all the time though. We had the car checked and two codes came up 1 #543 stating the Fuel Pump did not have enough pressure/low voltage battery. We replaced the Fuel Pump, the Fuel Pump Regulator, and the FUel filter....it didn't correct the problem. Another code for the Tranny is coming up it stating the 3rd gear ratio. Could this problem really be in the transmission or does it sound more like engine/electrical problem? Any help in determining what's wrong will help.