It turns out that this is a major problem for Lincoln LS owners being that this vehicle line was a joint venture with Jaguar. The PCM (electronic control module) had know issues prompting a PCM upgrade program. Because the PCM malfunctioning controls the coils causing them to misfire and the trans to shift poorly, the transmission prematurely gets damaged and multi engine codes. It also can lead to catalytic convertor damage. Sensor problems abound.

My trans shop had fits getting the proper parts to rebuild the trans and I ended up having to take it to a different shop afterwards because the PCM was also bad as well as requiring a new solenoid pack! It turns out that the PCM has been on national back order for several years and I had to find one from a re-manufacturer (AES). THIS IS RIDICULOUS! A known problem with the PCM and to have it not be available because so many are being replaced. Why isn't FORD standing behind their product? Its costing LS owners thousands of dollars in repair costs!!!!!!!!

Update from Jul 24, 2014: Fast forward one year and hear we go again a PCM problem!

I AM SOOOOO FED UP WITH THIS CAR AND FORD!!!!

My PCM is bad again!. Fortunately it is under warranty. However since I purchased it independently from a re-manufacturer I had to have it removed and sent to back to be repaired. More bad news, it's not repairable and initially they don't have one to replace it. Four days later they find one but it has to be ordered and programmed. More days pass and I'm now on week three of paying for a rental car@ $30 a day!

I had gone into a Lincoln dealer to ask what I should do, they had no answers. They had a guy who's been waiting 7 weeks for a PCM. At least the trans is not damaged again! I still have a coil issue on cylinder 2 (under manifold) and I have error codes on both catalytic convertors all thanks to the PCM! THESE CARS ARE LEMONS!!!!!!