Joe just switched to an MSD distributor, so that cap won't work.
Joe, I can't comment because I have a Medium Riser intake, but I know it's close with that intake and the HEI terminals. Very close. Just a guess, but I don't see how it would fit. The standard terminal cap, #8437, will gain you a little bit of clearance over the HEI, but not much.
Edit to say that I forgot you said you were using the stock air cleaner. Do you mean the stock Mustang air cleaner? If so, then you can disregard everything I said. I use the Ford aluminum air cleaner and don't know how much difference in height there is.