A misfire can be caused by loss of ignition, fuel or engine mechanical issues. Check the basics first make sure the engine has "even compression" (intake /exhaust valves sealing well), compression and cylinder leakage tests will confirm engine mechanical integrity. Also check that the engine produces approx 21 inHG vacuum at engine idle when warm). You could have a vacuum leak (intake manifold gasket or small vacuum hose near that runner in the intake manifold). A misfire in one cylinder can be caused by a restricted or clogged fuel injector not supplying sufficient fuel to that cylinder (low fuel pressure or volume due to a bad fuel pump would affect all cylinders). Loss of ignition to a cylinder will cause a misfire (spark plug, ignition coil. plug wire coil pack, or triggering of the ignition coil issues all can cause loss of ignition or weak ignition to a cylinder). I like to look at freeze frame information, live sensor data, and Mode 6 information on a professional grade scan tool to look at fuel trim values long and short term, engine vacuum and other key sensor data that can be read right of the scan tool without having to do intrusive testing at each sensor.