Ok, here's my weird options on this situation....
Like already mentioned, a shorter air filter is the cheapest solution. That way you get to keep the rallye hood.
If you absolutely need to keep the 3" filter....
Aftermarket fiberglass Cuda hood with a Six Pack scoop or get a flat hood and cut it for a shaker but have the shaker bubble attached to the hood. This way you PERHAPS may get the clearance you need plus get some fresh air with a semi stock look. It depends what look you want.
You can also go for a Ram Air box that has the hoses that lead to the front of the car that allows cold air to be drawn in...
http://www.summitracing.com/parts/SPE-728/What ever you do, see how much clearance you have with the hood you use to avoid any
and
.