Belknap Subaru is mod friendly.
I'm not sure exactly where it is, but it's somewhere in Belknap county. So, central NH. But whatever. Check the "install uppipe in NH" thread. there are links to their website.

 

No one is going to give you more than your Civic would be worth without modifications, and most dealerships will give you less because of it. Return it to stock and sell off the parts if you don't want to take the hit. In regards to Subarus, Exeter Subaru is friendly towards those with modified cars.