If it fits the carb, use it. if not the only absolutely critical thing is to seal the top of the carb to the base of the air cleaner. if the hole is on the "dirty side" you can just use a piece of tin, duct tape or what ever... but you dont to suck dirt into the engine under any circumstance. An open element air cleaner will cost you warm up time and some cold weather driveability... but dust sucking in would kill the engine pretty quick.Yeah I figured that out last night, I guess I probably won't be changing the manifolds then.
You saying I should keep the stock air cleaner box? I think I actually need a new one though, the back of the box was cut open to accommodate an aftermarket cruise control that I almost immediately got rid of. Now the hole where they cut into the box is covered in electrical tape. If I could locate an air cleaner box that is close to stock and fit the new carb I'd definitely go that route though.