I've replaced spark plugs, tps, iac and cleaned the mass air flow sensor and throttle body and the sensor that reads the intake pressure, and both oxygen sensor. The cat has been gutted out for about 6 or 7 years.
I still get a random misfire on all 4 cylinders. I've replaced the coils too but that didn't fix the problem. The problem happens every morning when the car is cold, and I t stalls when making a complete stop. After it is warmed up it runs like a champ.
I think before undertaking any more work it's best to do a full scan and check for any codes and then check the live data to see if the parameters are all in the expected range. Checking the usual air/fuel/spark related parameters and also performing a compression test will give you a lot more info otherwise you might be wasting too much time and money replacing unnecessary parts.
Clean the fuel injectors and intake valves. I use Marvel Mystery Oil in the gas tank at a treat rate of 1 oz. per gallon. After 1/2 tank of driving locally, I add Berryman's B12 (2 oz. per gallon) and immediately drive the car full throttle on the highway, 45-75 MPH, six times minimum. Continue driving on the highway until the tank is nearly empty, because the Berryman's evaporates from the gas tank after 24 hrs.
Repeat this procedure for three tankfuls (about 1k miles), or up to 3,000 miles in stubborn cases. The cleaners work best by cycling through "wet" at low, stop-and-go speeds, "soak" by shutting car off for ten minutes, followed by the high heat & pressure of highway driving/wide-open throttle. You can also apply heat by shifting the car into "L1" (or "D1") and driving 30-35 MPH for ten minutes.
I don't know what gutted out means without context but if the car has been sitting for a long time (6-7), that is most certainly the cause. But if it has been sitting you should always change the gas out in the tank before starting it as it most likely has deteriorated into sticky goop.
Since you didn't post codes, I can't help there but cleaning the MAF sensor can actually cause issues if an improper cleaner was used.
Generic
Since you've already replaced basically everything, you should start by adding the fuel system cleaners. You should also use an engine cleaning oil additive in the oil and then change the oil to a high quality synthetic.
K24 Specific
After that, if you still have an issue the suspect is valves not having the correct clearances. IF you hear a light tapping noise while the engine is running, that is another sign. Some of the K24 engines had issues where the valve clearances got too tight over time (they loosed up when warm) and had stalling issues. This was more common on the Honda Element and CRVs for some reason.
Sounds like you have a head gasket seeping a little between a couple intake valves causes a lot of miss fire until motor gets warm or hot .heads expand when hot tightening up the gasket letting little leak seal untill cold . That would not interfere with compression test most of time unless it blows out. Why don't you try a can of head gasket sealer or best is called k w block seal one can mixed up with 3 quarts water drain radiator put it in run about book said 20 I usually drivrmit about a hour turn it off cool down about 4 .If it's that you'll be Good to go . Just my opinion be there before hope you have good luck
stalls on a stop you say, i would check the brake booster vacuum line, its probably cracked. if you notice any change in rpm, any at all, when the brakes are pressed then i would start with the brake booster vacuum line for sure.
also maybe spray some brake clean around the intake tract and see if the rpm changes at all that would indicate a intake leak another possibility.
and last but not least check the fuel pump power draw, i dont have a factory service manual for than new of a civic but i know they can be found online and they will have a very good trouble shooting tree.
You should have 2 coolant sensors on it. One is for the temp gauge and the other one is to tell the computer if the motor needs extra gas because it's cold or not warmed up yet. Just like the old cars or lawn mowers or any other combustion engine, you have to choke them to get them started. The old cars had a spring loaded choke and as the motor warmed up, the choke slowly opened more and more as it warmed up. Both sensors are called coolant temperature sensors, you just have to know which one does what so you can buy the right one. If your sensor has more than 2 wires going to it, then it's possible only one sensor is doing both jobs, but it has to have more than 2 wires in the plug. Once you replace that sensor, your other problems might stop as well because it also tells the computer how hot the motor is, therefore it plays a part in your timing advance, fuel injection leaner or richer, etc., etc.
Determine if it is one cyl causing the problem by disconnecting the injectors one at a time (as it is misfiring). If a cyl doesn't change the way it runs as much as the others be sure the compression is within 10 psi of the others. If it is then possible vacuum leak at that cyls intake, valve adjustment or the injector? If all cyls make the same difference its either a vac leak (affecting all cyls), valve adjustment, coolant temp sensor or dirty injectors.
