You'll never get back what you put into it and it's a lot harder to sell a hybrid because there are very few buyers out there interested. Most people hear a cars been modified and go looking elsewhere. If you can find a buyer who understands what he's buying and assuming you've spent the money and done a good job, I'd say you'll probably get around 65%-75% back. That buyer will be hard to find and most hybrid have better luck parting everything out.

What year Civic are you planning to swap? I'm assuming a '92-'95, but the problem with those is there getting old. The cars themselves aren't worth that much anymore. You can find a decent one for $2000 nowadays (even less if you take some dings).