Dear @burnoutrevenge
Ok let me tell you a process of trouble shooting this problem with the help of your mechanic .... I can guess there is a failure in flow of current starting from coil to cylinder combustion chamber.... a civic has 4 cylinders having four plugs deep inside and 4 long tip injectors on the top of the plugs and easily can be seen after removing the plastic top cover....... the current produced by the coil flows till spark plugs through injectors ...... ( now we have to trace either the plug or injector is faulty )
Get the engine start and then start removing the injector far from the plug .... If a car is in completely ok condition, car instantly start vibrating and shivering due to non functioning of one cylinder due to lack of current which means plug and injector is completely fine ...... ( repeat this process for all the 4 injectors and plugs ) but in case of a problem like your car what happens is that in one of the injectors nothing will happen which means even after putting the injector apart from plug car will not shiver and vibrate because there is something already faulty between the two either injector or plug ...... so after finding the problematic injector and plug combination, take both of them out for inspection ..... now change that particular plug first and then again start the car for trouble .... hopefully issue will be resolved but if still gives missing then change that specific injector
with the change in the faulty plug / injector the current starts flowing till the end of the cylinder and the missing will disappear