1988 Pontiac 6000 not sure how to adjust timing

Car has a v6 with a distibutorless type ignition, someone removed what would have been the distributor to install a new seal. But since it does not have a distributor I dont see how this could cause the timing to be out as the shaft that is there as far as I understand is only used to drive the oil pump. However after changing all the coil packs new plugs and wires it still runs rough and has a miss. Any help would be greatly appreciated.