2006 Peterbilt 387

PROBLEM: MY ECU is not communicating with the Transmission ECU. The Eaton fuller transmission is giving me code 35. When the Truck starts it idles fine and as soon as it tries to find the engine speed about 20 seconds later it begins to rough idle. The speedometer bounces back and forth from 25 to 60 mph and then settles after 20 more seconds on 25 and stays there. The cruise control and jake brakes do not work. When driving I have to rev the engine up high and let is drop down in order to grab the next gear. It will shift through all gears up and down but I believe that may be a fall back setting.