cylinder #3 misfiring

I have a 1999 Tacoma TRD 4x4 with the 3.4L V-6 automatic. I have blown 2 spark plugs out the sockets and had to install helicoil thread inserts. When I completed the last helicoil repair I had a misfire in that cylinder. I replaced all the plugs and still had a misfire. I moved coils around and still had the misfire in the same cylinder. I have moved coils and plugs around and still have the same misfire. The last thing I did was replace the classis ground which was frayed but still have the same misfire. I feel like my last things to check are the ignition control module or the computer. Anybody had a similar problem and how did you fix it?