MY 89 civic dx randomly is hard to start,I have replaced the main relay, fuel pump,plugs, cap and rotor.It runs top knotch, usually fires up right away, but every once in a while is hard to start.The relay I replaced was a $40 knock off rather than the $130 honda, it is also smaller than the original,I don't know if this matters though, as well I keep getting trouble code 16.

Replace the ignitor and coil:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-46563-4.html#post265896

DTC 16 indicates a fuel injection problem. See if you can head each injector click, when the engine is running. If not, check resistance of the bad injector and replace, if necessary.