I have a '99 Civic DX with a JDM B20B swap. For the Exhaust set-up I used a the stock B18B Exhaust Manifold with the Integra LS Cat. I am trying to mount up a Civic Hatchback exhaust and there is about a 1-2" overlap.

I have to run a Cat for emissions.

I'm planning on getting a header later on, will I run into other issues?

 

Yes. You will basically have to start over with your exhaust idea. Go aftermarket first and start getting ready to fab up a custom length cat with testpipe to go to the rest of the exhaust.