1999 Mercury Cougar misfires

My car was misfiring. I put a code reader on and found out the it was misfiring in cylinder 4. I figured it was a botu time to do a tune up so I went out and purchased 6 new spark plugs and a new set of wires. I hooked them up and the engine didnt seem to run very well. Not much power and hesitant. I ran the code reader and was getting nothing. Then when I parked the car and let it sit idleing come codes came up. No longer was cylinder 4 misfiring but now cylinders 5 and 6 are misfiring not only that but some smoke was coming out of the back side of the engine underneath the ignition coil. Im not sure exactly where it came from but now it sounds like a knocking sound in my exhaust. Any suggestions?