We don't know for certain which emission component your Honda Civic's new VTEC engine is missing but apparently the problem is that your Honda's original ECU is not built to be compatible with the new VTEC engine. Your option is to either upgrade the ECU to match the new VTEC engine, or if possible find the missing emission component and install it on the new engine; so that you may have an input to provide the old ECU.
If you use a trouble code scanner you'll be able to find out which emission component is missing and start from there. Email us back once you find the component in question and we will assist you further.