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I have a 97 Honda Civic EX with 163K miles. I recently had my transmission replaced which is when the ignition problem started to occur. The engine was running perfect when the car went in for the transmission. After getting it back there was a slight but noticeable misfire. This misfire got continually worse over a one month period, eventually leading to the car not staying on (also, toward the end, a loud banging sound coming from what I believe was unburnt fuel hitting the cats in the exhaust). I do not believe in coincidence so I am wondering what my mechanic might have done, intentionally or unintentionally to cause an ignition misfire when replacing the transmission.

Any advice is greatly appreciated, thank you.

 
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Also, replaced plugs, wires and rotor to no avail.

 
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yea that's not right its a simple drop and replace from underneath he had to of touch something besides tranny do your timing belt water pump and tensioner and see if it goes away he might have advanced timing on the crank a tiny bit past the two arrows to make it seem like a misfire when i changed my very first timing belt on a civic that was the result in my inexperience with interference engines when i first started but first because thats a big job check your cap or rotor again it could just be loose make sure all the screws are in