Wiggle the air cleaner box. Its intended to be isolated from metal by rubber at all mount / contact points. If not, they can make a lot of noise. Also check the long bolt-on braces between core support and strut towers. Those have to be good and tight, can't have any stripped threads. Of course look for anything very close to the firewall too. For what its worth, new rubber or poly stuff can go bad pretty quick especially if leaked on so don't rule anything out. I'd probably re-check any recent work too, unless none of it has had any effect on the clunk.
