They don't clear the stock airbox rubber very well either, I had to clearance my hood there to avoid the rubber wearing out....Also had to shim the upper bolt on the hood pins so the thing would clear the front hood seal area and sit down properly.

oke:
WDK to the rescue.
When you say rubber, do you mean "plastic"? And are you referring to stock duals, or stock single?
I guess I got lucky with my carb setup and diablo hood. Running Riva conversion manifold, BJ 46, wamiltons OEM FA adapter, and stock single 44 FA plastic lid and screen. The plastic lid barely clears my cylinder head.
I have read about people having to do that shimming also.