Problem after smog check

[Meka]

I took my 84 Carrera in to be smogged last week. Soon as I got it home I realized the engine compartment lid no longer latches. But thats the least of my worries. The next morning when I started the Carrera I noticed a weird thumping noise under the rear of the car. Kind of a basey reverberation. It makes the noise for about 3min then stops. Only make the noise when the car is cold. At first I thought it may be a heat exchanger but now I am thinking it may be something more sinister. Any ideas?