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Keep the shaker for apearance only. I'm sure when you're revving the engine with the blower that shaker will be moving like crazy! That will get some attention.
I think that all you need to do is change the way it's mounted onto the engine. The Saleen S/C isn't that much larger than the stock GT plenum to my knowledge. Put the Saleen S/C in and then find a different way to mount the Shaker scoop and run the hose and it should work.