Cracks in the exhaust manifolds are very common on the Civics of that era. They usually crack where the exhaust runners meet the mating surface where the manifold bolts to the engine. they are typically very visible. if the manifold is cracked, your best course is to take it to a muffler shop and see if they can weld the crack shut. Otherwise, you need the manifold and that manifold includes the catalytic converter so it gets very pricy.The other possibility is that the heat shields for the catalytic converter or the under car heat shields are loose or broken. That is also a common condition on the Civics of that era. My advise is to let the car sit overnight, then open the hood, start the engine and go up front to listen to where the noise is coming from. If its higher in the engine compartment and from the front it is probably the exhaust manifold. That will make more of a ticking noise than a rattle. if the noise is lower towards the front, it could be the converter heat shield. If the noise is lower and towards the center of the car it is the heat shield for the exhaust system.on some Civics of that era the exhaust manifold was covered for 10 years/150,000 miles under the emissions warranty. if the car is out of that time or mileage you might want to ask your honda dealer to see if honda will pay for it as goodwill provided they confirm that the problem is with the exhaust manifold.\hope that helps