Engine backfire

I just changed out the spark plugs and wires today after I started to get a misfire code for cylinder seven a few days ago. I did it one at a time so then that way I do not mix up the firing order. I did have to remove the air cleaner box to have better access to the passenger side spark plugs and used WD40 on the spark plug on cylinder three. I did not move anything else around or take anything else out. After I finished I went to start it up and it would crank but would not turn over. I then went back and rechecked my work and realized that I ended up putting the wrong wires on the wrong plugs on the driver side; after I switched them to where they were to be it started right up, but now has a rough idle and backfire sound, the sound goes in threes 1) loud, 2) slightly low, and then 3) when it is almost faintly heard. What could I have done wrong, or what kind of suggestions would you have to help me fix this problem?