2000 Lincoln LS Transmission Problems; someone please help!!

I have a 2000 Lincoln LS with 130k miles on it. When I shift it in to reverse, sometimes it takes up to 10 seconds to engage, and when I'm driving it in D5 it will start out in 2nd gear. It also hesitates to shift from 2nd to 3rd. When I am driving around town it will start to smell of burning transmission fluid from the air vents, and all of the sudden "Check Transmission" Will appear on the dash.
Can Anyone help?!

Welcome to the forum!

Since you are getting a "Check transmission" indicator, there will be codes. Your standard OBD-II code reader may or may not be able to pull these codes, but a high-end scan tool with the transmission software will be able to, and these codes will likely point you in an appropriate direction.

I would suspect you have either an issue with a speed sensor or shift solenoids that are sticking. I believe that your LS has both an input shaft speed and an output shaft speed sensor. If one or both of these sensors are in error, it can effect shifting. I'm not sure that they would effect delayed reverse engagement.

There was a Technical Service Bulletin for "Delayed/Harsh Reverse Engagement" that applied to the 2004-2005 LS, TSB 05-21-8. You may want to see if a similar TSB exists for your 2000. The solution is to replace the solenoid body once the condition occurs. There is an additive for the transmission that is supposed to prevent the condition from happening, but that additive was not installed in certain vehicles.

-Rod

Like was mentioned get the codes read and go from there. You don't mention anything about fluid/filter changes. IMO thats one of the best ways to maintain a trans. You may want to do a fluid/filter change and try a bottle of auto-rx or sea foam trans tune.
www.auto-rx.com

Thanks a lot for the help. I'm going to try to change the fluid first and see what that does. I know that this is a sealed system so it could get complicated, but I found a site with a diagram of how to do it
http://www.charlietranny.com/5R55Nfluidfill.htm

I'm hoping I don't mess things up, but this is all I know to do
since I've scanned for codes and nothing comes up.

Does the scan tool you used have the software to scan the transmission? As I mentioned, the common commercial scan tool won't be able to access many of the transmission codes. Since the transmission light came on, there will be a code. But, since it was the transmission light rather than the Check Engine Light, you probably will need the tranny software rather than the powertrain software.

-Rod