I have a 96 civic ex, with a 1.6 vtec swap. My uncle just did the swap ove the summer and it was working fine for a while.. my CEL has been on because of evap emissions, so I never really paid attention to it.. but it started blinking, I checked it w my scan tool, cylinder 3 misfire.. I take it to a mechanic(im just in schol for it now), and he replaces spark plugs, which I had just done that day, and I'm not sure if he replace the distributor.. I'm not sure if my car has coils to replace or not though.. I was reading up on a 96 civic you were helping before lol.. but wtvr, the mechanic fixed a harness that was eaten away by the belts. So it was running so so, I didn't notice the CEL blink for a day and then it comes back, I take it back and he says to check the timing belt.. I'm guessig the timing belt as positiond at TDC, because I did that myself. And my motor hasn't blown up.. then I added a AM air filter hoping that extra air and fuel will een out the car, which isdid AWESOMELY for 2 hours, and then it got eve worse.. Today getting and going from school I could barely press the gas without making the CEL blink. OH best news of all, now 1-3-4 are misfiring... please any help... I can't afford to pay a mechanic to do more of nothing

. Replace the Ignition Control Module (ICM) and coil, if the mechanic did not install a new distributor:

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

If the mechanic installed a new distributor, find out the brand. Over 50% of new aftermarket distributors for Hondas don't work at AMHD. Only use genuine Honda distributor housings--aftermarket ICMs and coils are fine, however.

. In Hondas, only use the same NGK spark plugs that originally came in the engine.

. This link should help:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-11.html#post2028083

. Get rid of the aftermarket air filter, especially if it's the oil-impregnated type. Go OEM. Don't inject too many variables into the equation.

. If the problem persists, remove all the spark plugs and check each cylinder's compression--it may indicate burned exhaust valves, which can cause misfires. Usually, this happens if the valves are adjusted too tight.

My bet is replacing the ICM and coil will solve the problem.

I took out the after market distributor and put a honda one in, mechanic took out the spark plugs I had just put in and said they weren't good for my car and replaced those too

Oh, and the mechanic changed the ignition rotor? Don't know what that is though

And I put oem intake back in, and the car barely went up hills, got to about 30 mph on the hill, and started decreasing mph slowly.. thanks a bunch for your time

Overall, then, is the car now running well? It's unclear to me.