You need to get your catalytic converter hot enough to light off. That's easy to do when the cat is built onto your manifold, but you've moved it much farther from the engine where the gasses are cooler, and replaced it with a lower restriction, cooler running catalytic converter. A hi-flow cat on a civic is really overkill. Using a standard OEM cat will probably allow you to pass the test, and should still bolt up with your aftermarket parts in place of the hi-flow part. Not all civics have the manifold-type cat, and you won't find a cat in a junkyard because it's not legal for them to sell them. Maybe you can find someone locally or on a message board that will part with theirs, or let you use it for a while. I don't have one, but I've gone through the same thing with my civic.