This Dual quad filter, will stick through the hood by an an inch and a quarter. So, I'm thinking an inch clearance around it. Too much? Will be cutting the opening the same shape as the filter.
I would think that if you're going to chain the motor or put some other form of movement limiter on it you'd be OK. The higher the position of the intake/carbs/air cleaner, the farther it will move. Without some form of limiting engine movement you'll probably still be OK, but I think I'd test it before totally finishing the hood. - No sense in marring the body work.
Make sure the hood doesn't catch on the lid as it opens. We really were surprised at how much we had to cut for the extra clearance as the hood rises, but we're sticking a lot further through.