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Hey, I know that any motor will go in any car with the right amount of money and know how. So I guess I know the answer to my question, but my real question is how difficult would it be, and how much money would it cost. My application would be to a 1999 Civic.

 
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Yes, you could swap it out with a B18C from a JDM Integra or a B16A from a Civic Type-R. But your best option(bang for your buck) would probably be to swap an integra GSR engine/tranny/mounts/ecu into your civic,the harness should plug right up and mounts will bolt right in. With a few bolt ons it can make as much or more power than the Type-R engines. The only thing that would make it difficult is if your civic is not an Si, then wiring will need to be done for Vtec to function as it should. If i were you, i would go with a 1998 or so Integra GSR swap. just so you know, your car is OBD-II so make sure when selecting a swap your getting an OBD-II GSR swap.