I have a 2000 TL with about 174k on it.

Last weekend I drove the car home for Christmas and it was fine. The next day I go to drive it and the battery is just dead. I was busy so I said I will deal with it after Christmas. Today I had AAA come put a new battery in and everything seemed fine until I started driving it.

Now the idle is rough and the car won't shift out of first gear. The car goes fine, but won't shift. Obviously I can't get much speed only in first gear.

So my question is if a car sits that long with a dead battery does it ruin something? Or is this a coincidence?

 

letting it run a battery all the way down was the main problem here

Simply remove -wait 1 minute- and reinsert the CLOCK fuse on passenger end of dash to reset the ECU
Low voltage results in false codes and engine weirdness

then you should be able to drive it normally for 30 minutes with no load ie: no headlights or stereo use- to fully charge new battery- they are not full full when you get one!
then drive to a parts store for a free charging system test.
Might be alternator involvement depending on how long battery was bad and car had to depend solely on alternator to operate all the systems = not good