cut the hole in the decklid first, then bolt it on.. I'd suggest putting some bondo around the edges to make it look like it's molded into the decklid. as for the underside, you could probably take a dremel to it and clean it up, and if you were planning on showing the car etc, you could even grind away at the decklid plastic so it's flush with the inner edges of the scoop, and then bondo it so it's smooth.. then repaint it. did that make sense? you also need to keep the EMI plate, that needs to be relocated to the underside of the scoop. I'm not sure what the best way of attaching that is.. rtv?? something higher temp?
Another option for the underside of the decklid, is to splice some heater tubing, and fit that over the edge of the cut material.
hope this helps!
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steve@fieroproject.com
http://www.fieroproject.com