I cannot answer with certainty that your HEI will fit because I have the MSD ready to run which I believe is a bit smaller.
But the MSD fits beautifully. I have the 3 inch regular sandwich type air cleaner. I have not permanently mounted the air cleaner since I am still working on the engine but during mock up the hood closed without hitting. I was lucky because i have open hood scoops, I was able to watch the hood go down to check if everything would fit.