DISCLAIMER* I have no expertise in Third Gen Civics, or D16A1 (ZC) engines.
Without doing much research, I would think you'll probably need engine mounts from a concurrent Integra, although the stock engine mounts may work. Also, you may have to do some extensions in the wiring harness, because of the slightly larger dimensions of the DOHC head vs the SOHC head. Then, you'll probably need a custom intake and exhaust, as well as the proper computer to run the D16A1.
There are a couple of people on the forum here who are really into ZC's and older Civics, so I would start by doing some searches here. Also, you can get a pair of quality service manuals for the Civic and the Integra to compare wiring. Or, if the car is not a daily driver, pull the original engine, set it on a pallet or concrete, and use a plumb bob to take measurements at the factory engine mounts. Then take the engine mounts off, and see if they fit the D16A1, then measure again, and compare the two sets of measurements. While you are doing that, you can remove the electrical harness from the stock engine, and start draping it over the D16A1, to see where it fits, and where it doesn't.
So, either continue doing research to gather more information, or start pulling things apart and doing physical comparisons.
Good Luck! And, again remember that I am no expert with this chassis.