Ok everyone I'm new here. So I'm learning how to post. Hope I can do this. I'll try to as brief as possible, but details are important in solving this problem. First off I had the identical same problems as Freejay. Could not use a code reader, the port was dead. No gear shift indicator lights. This just totally blew my mind away. I was so close to finding my problem. But frustrated I gave up the ghost and took the truck to the dealer.
The Dealer put the truck on a WiTech scan and found the PCM (Powertrain Control Module) was dead on the Buss. So they trouble shoot the system. What they did was checked powers and grounds to the PCM and I had no power to either of the A209 pins on the C1 connector. They disassembled the connector and found heavy corrosion and open wires from the corrosion causing issues. So what they did was replace the C1 connector and replaced the corroded wires. Some of the wires were ok and did not need to be replaced. I knew some the wires were corroded, and I kept trying to use baking soda to clean the pin clips that are soldered to the each wire. But I was having no luck.
So to sum it up they replace the C1 connector with a new one and replace a few wires and soldered the replaced wires to the old wires. Also they checked the other 3 connectors to the PCM and no corrosion was found. They did not have to do any programing to the truck they fired up the Truck and it started perfectly. They did scan for codes and none was found. I did find before I took the truck to the Dealer that the Wiper Cowling was leaking water and the reason it was leaking the seal was not put on correctly at the factory. The water was dripping directly onto the PCM C1 connector causing the corrosion. This maybe rare but if your Scan tool can't come on to the buss and see the PCM, your problem may be like mine or Freejay's. Replacing Connectors is not a big problem I had mice get in to my Mercury Marquee and eat a lot of the wires. Took me almost two weeks to re-wire the car. Amazon sells the pins in a kit so that you can pull the wires out of just about any connector. And if you need to replace a connector you can get them really cheap at a Junk yard. Also if you look hard enough you can find New connectors at a number of companies across the internet.
Thanks, Freejay for posting your problem, it lead me in the right direction.
I surely hope this helps someone, it about drove me nuts. Lol. I was so close to fixing the problem myself and saving the $720.00 dealer repair bill.