Ok guys I have been chasing this problem for about a month and cant figure it out.

Background on the car. Bought a 99 civic ex with a blown motor. I put in what I was told to be a low mileage motor with the head off the original ex motor. Installed the Y7 motor and trans 5 speed into the car. Car has a cold air intake and fart can exhaust with test pipe.(it came that way)Behind the test pipe there is a hole in the exhaust That needs fixed but I haven't had time to do that. When I first did the install I had a very little misfire and didn't think anything of it.

I took it in and had the codes pulled when the car stated getting a really bad idle surging and the occasional flat spot while driving. They pulled up misfire all 4 cylinders along with knock sensor and IACV code and secondary O2 code.

Cleaned the IACV to no luck and replaced it with a new one along with plugs and wires. Problem continued.
Today I installed new injectors, cleaned the throttle body and replaced throttle body gasket and a new fuel filter. Problem continues and almost seems worse now.

Im to the point now that I don't feel that I can drive it the 140 miles a day to work for fear that its going to leave me somewhere.

The flat spot is kind of hard to describe other then when driving at speed it usually feels like its not getting fuel and then it starts getting fuel again. This is the reason that I replaced injectors and fuel filter and cleaned the throttle body today. I am also still fighting idle surging. I have tested for air leaks with carb cleaner and haven't found any leaks.

Any ideas or other things to look for would be great. Im lost and cant just keep replacing parts.

 

I forgot to mention odometer shows 172k and Im pulling between 35 and 40 mpg on any given fill up.

 

Just got home from getting engine codes pulled this morning. All codes the same plus
P1399. I really hope this helps someone so I can get closer to figuring this thing out.

 

taking it to the dealership tomorrow to get this figured out

 

Keep us posted on what they find.

I'm fighting a misfire issue similar to yours right now. I just replaced the spark plug tube seals, as a couple of them were really bad and the tubes were filling up with oil and I was thinking that could be the culprit, but I'm still getting some misfire on start up for a few seconds, then the engine seems to smooth out.

My next step is to replace the plug wires, I'm not sure how old they are, and being 'submerged' in oil probably isn't the best thing for them.