MAYAman,

It sounds like you may be contacting your hood with the box. Get some non-drying modeling clay and make some cones about a half inch tall. put wax paper on the air box, place the cones in a grid about 8" to a foot apart. Make sure there are some near the corners of the air box. Cover the top with another layer of wax paper. Then close your hood.

Re-open your hood and check the condition of the cones. If any are smashed completely, then your engine is pressing into your hood and transmitting the vibration to the rest of the body. If that's the case, you may have to think about either altering your hood, or the box.

Looks good though.

Cheers!