Could be the coil.
An easy way to find out, if it is an aftermarket coil, is you can put the stocker back on, if you have it, and see if the problem goes away.
On the other hand, a miss fire could be the coil, the wires, the plugs, a dirty MAF, bad/worn cap or rotor. The list goes on.
Do some visual inspections and diagnositc testing to try and find the source of the miss fire.