Basically I'm at a crossroads building my 302. Should I get a high rise intake manifold and cut a hole in the hood for the air cleaner, or put a dual plane and put a smaller air cleaner? The car is only gonna be driven on nice days with no possibility of rain, and I have never seen a mustang with the open hood.

 

For a driver and cruising car go with a dual plane intake.

 

aircleaner through the roof is something for the dragstrip. if it's not going to be driven in bad weather you seem to like your car, so why chop the hood.
i'd say as well for driver go dual plane

 

Unless you have a blower sticking through the hood, no one does that anymore. That's why I have that "bubble" on my hood, to keep everything inside the engine bay.

 

Air cleaners that stick out of the hood that aren't in a scoop are a really good way to screw the carb metering all up. They meter fuel based in airflow INTO the carb...not across the top of it. And by high rise, do you mean tunnel ram? You don't want that on a street car, or most anything short of a full drag race car that turns a lot of rpm.