When you replaced the plugs did you notice if the plugs where coated in oil. If you have oil getting into the spark plug tubes you will need to replace the valve cover gaskets to fix your problem and then pull the plugs out and put them back in to remove the oil in the spark plug tubes. This is a common problem on many vehicles that I run into.
What are the codes that are showing up now since all this work has been done. Is it just the misfire codes or are there other codes showing up. Also what codes were there when the problem started before you did all the work you have done to it so far.