Check the maf load and also the commanded afr while the engine is misfiring, compare that to the data pid of the afr sensor, you should be able to figure out the culprit.
A hanging pcv valve or a cracked hose for the pcv can cause such too, so first isolate all vacuum users to verify they are not muddling it up before you check the pids.
Usually black smoke is due to a wrong reporting maf, a maf that has been murdered with cleaning sprays: combined with open loop cycle, you will have black smoke and a faulty run, it will also not complete an ecu obd readiness cycle.