I'd be willing to bet it's a mystery plug that several people have on their cars. They are for other factory options your car may not have. But without seeing the pic, it's my best guess.

I am still leaning toward a vacuum leak. Did you check your EGR tube? It's the accordion piece going from your lower intake manifold to your EGR. It is mounted under your throttle body. It has to be removed or at least moved when you do a LIM job. I'd assume the piece is fairly fragile, nature of the beast.