This must be a great idea because I plan on doing that to my car, too, ha ha! (I'll need to do this when I remove my bellhousing next to align it better) If it helps inspire ideas even though I haven't built mine yet I plan on making mine with an overlap of the sheet metal and using rivet nuts so I have an easy way to thread bolts down from the interior of the car. I'll use something like a 3m weather stripping putty to seal the panels yet still be removable.
Here's an example of them from amazon if you're not familiar- these things are awesome and are available in many thread sizes.
http://www.amazon.com/s/?ie=UTF8&key...l_12ywgmbnmw_b
Hope this helps!