Uuuuuummmmm it hard to tell with out looking at the car really
If they have changed the coil pack and leads and plugs.
There are a lot of other things it could be :-(.
I would check the bypass valve anyway if the car is down on power or gutless it could be Good place to start but.
But it would not throw up a misfire code unless there were other things wrong with the car.
When was the car last serviced ? Is it a standard MCS
I would get you fuel pressure checked on the fuel rail. you my find the fuel filter needs changing and i would also get the injectors checked and cleaned.
You could put a can of fuel treatment like BG44K in it see if it helps if you have a bad injector but if there bad there bad and normally need clean properly
Hope this helps