So you have replaced, the wires, cap, rotor and plugs, and that made no change. So unplugging the injector on #3 made no difference in how the engine ran so you replaced the #3 injector, is the new #3 injector releasing fuel? You can use a long wooden dowel (you can also use a long screwdriver) and place it on each fuel injector and put the other end to your ear to listen for the pintle valve opening and closing. If the fuel injector is working then you should hear the clicking sound if not then the issue is most likely the wiring since you have already replaced the fuel injector. The issue is most likely the connector at the fuel injector, the connector is not that expensive and easy to replace. There is a tool to check fuel injectors that works on the same principle called EFI quick probe, but it cost around $100. As long as all 4 spark plugs are firing, all 4 injectors are releasing fuel, the misfires should go away. The only thing else that can cause a misfire is valve clearance being way off or oil fouling the plugs.