Considerations:

Some things to note before starting are that it will be easier to do the swap if you don’t want your air conditioning anymore and if you get a complete engine with all it’s parts to include the distributor and entire intake manifold with the fuel injection parts that are stock. Also note that you must use the proper injectors and the old ones will not work, as they are another type of injector that is incompatible with the 92-95’ ECU. You will have to jumper the check engine connector from now on to pull codes from the ECU so it is important that you install it and the data link connector or you will not be able to troubleshoot if you run into problems nor will you be able to get your engine certified by a state referee.

Also get a higher pressure radiator cap since the 92-95’ engine runs it’s stock radiator cap at a higher pressure than an 88-91’ Civic. It may be only due to the size of the stock radiator on the 92-95’ in comparison to the 88-91’, which is about half the size, but it will help your engine stay cooler anyways. It is easy to do and will let the engine run much cooler. If you go to AutoZone you can get an Accord / Prelude radiator cap that runs at 16psi instead of 13psi which is what the stock one runs at. They look identical and are usually hanging right next to each other. If you are having trouble finding it just find the stock one and look around next to it till you see the higher pressure one that looks the same. They say what they’re pressure rating is on the top of them.

Also you could go to a colder thermostat like I did. I found a 170-degree thermostat instead of the stock 195-degree thermostat. Since I live where it is often 100 degrees in the summer this helps a lot but if you live in a cold climate then just stick with the stock one. I also run Redline Racing’s water wetter to keep the temperature nice and cool find it at http://www.redlineoil.com/ . Their oil is probably one of the best on the market today also. Other than that just take time and look over your new engine and make sure it is in good order. Also get any parts you want to replace ahead of time so you don’t have to leave your car on jack stands for a week waiting for parts.  It would make life easier if you had the repair manual for both of the engines / cars and a good idea of what you’re doing before you start. Take your time and consult an educated mechanic for anything that you don’t understand.

Quick note: If you have a D16Z6 that is a manual then take the flywheel off of it and take it to the machine shop to have it resurfaced while you are doing the rest of the swap. Chances are that you will need it right about the time the machine shop is done with it. It usually takes 1-2 hours for them to do it. It is cheap insurance against a slipping clutch. The last thing you want to do is get the swap done and have to drop the transmission again to resurface the flywheel. If your D16Z6 was automatic in it’s previous life then you’ll just have to wait till you get the D16A6 flywheel out and then send it to the machine shop but don’t worry it shouldn’t slow you down too much. The 89’+ flywheels are the same and all use the same clutch disc and pressure plate. The 88’ flywheel clamping surface is smaller and the clutch is smaller and weaker. It is highly recommended to use an 89’+ flywheel and clutch. If you have an 88’ transmission then unless you get a newer one you are stuck using the 88’ flywheel and clutch.