If your car is a 4 speed, you need to change the axles and hubs to those from a 5 speed car. If yours is a 5 speed, you can reuse everything from your car now (not absolutely positive on that, but I'm pretty sure, never did one myself). It would be money well spent to get an CRX/Civic Si tranny as the gear ratios will be worth it. The D16Z6 tranny is useless to you. It's clutch is activated with a hydrolock system (like your brakes) while the older EF civic's use a cable system. You may be able to convert your car to hydro clutch, but I've never heard of one working 100% afterwards.

Other issues your going to run into is your fuel system. An HF is a dual point setup (2 injectors by the throttle body) while a D16Z6 is a multiport setup (1 injector per cylinder). You will have to convert your wiring harness over to MPFI (multi port fuel injection) to work. You will also need an proper ECU. Your best solution is to re-use the D16Z6's P28 ECU but it won't plug into your stock wiring harness. Some companies make and adaptor harness that will connect the two and leave the wires marked that need to be added. I've seen the adaptors before and I've heard they work well, but I don't know who makes them (HASport probably). You can also use your HF or better an Si EF ECU but you won't have any VTEC maps. You could create your own with a V-AFC, but you'll save yourself a lot of work with a P28.