2007 runs rough when put into gear but idles fine

[SteelB12]

So my girlfriend has an 07 Yaris sedan with auto tranny and between 100-110k miles on it. She told me today that the car would no longer go over about 25mph. The same thing happened a year ago and the shop where she took it replaced one of the ignition coils. Well, since the symptoms were the same, I figured the problem was the same. Doing some searching I found how to determine that one of the coils is bad. I replaced that coil. The car starts fine and idles fine.
Putting the car into reverse or drive causes the engine to stumble. Putting it into neutral has the engine return to a nice idle. The check engine light and service needed lights are on (were on before I changed the coil).
Replacing the coil was very easy. Did I miss a step? Is there something else I need to check? I drive a 4sp manual 87 Vanagon so her Yaris is a bit more complicated than I am accustomed to working on (I have replaced the water pump and transmission filter on her car last year)