I have a 68 400 with a 1" spacer and holley carb and Edelbrock manifold with standard 400 air cleaner on my 1969 bird. Had no problem with clearance.

That is how it was when I bought the car. I am going back to original manifold and quadrajet carb. Not sure if the height of the std vs. Edelbrock is different or if the carbs are the same so I cannot speak to that. But as it was it was fine.