My car rough idles at stop signs or red lights when in drive. It stops when I shift to neutral or park. Throttle body is cleaned, air filter changed, engine mounts changed and yet car still rough idles. What could it be?

What is your question?

One thing I have noticed is that the air box shakes a lot in Drive but stops in Neutral or Park. And you can specifically hear the rattling of the air box. Everything else is fine.

What makes this problem better or worse?

Shaking is worse when I turn on AC or heat.

How long has your 2002 Toyota Echo had this problem?

Almost 2 years