My 99 TL runs good however when I am at a stop light and the car is in drive it has a very rough and shaky idle, it stops and runs good as soon as i put the gas to it, It did this before and even after the transmission was replaced.

any idea would be great.

 

go to a parts store and have the codes read for free
how old are the spark plugs?- brand name if replaced?

done the egr port cleaning ?--since it should have gotten a recall several years ago for that prob- it still needs cleaning every 75kmiles, less for 99s
our system clogs easily with exhaust crud in a small passgeway and port at the cylinder
see diy section for help- 2 hours and 3 cans carb cleaner, 1 iacv gasket and 1 TB to manifold gasket