If you do anything and the noise stops, then it isn't rod knock. Real knocking doesn't go away without rebuilding the engine, so if you unplugged the coil and it it stopped then it isn't knock. Post up a video of the noise, it will be easier for us to tell you whats going on.
And for the misfire, your injectors are probably going bad. Pre-1992 cars had old style injectors that are prone to failure due to the ethanol in today's gas. The best option is to upgrade to new style injectors, they sell a conversion kit for ~$100. If you look at your injectors, you can tell if they are old or new style, old ones had square connectors and new ones have oval connectors.
Don't pay attention to the color, but you can see where the connector part is different between the two. You can Ohm test your injectors with a multimeter, each one should be between 10 and 14 ohms.