What is causing my 3rd Cylinder Misfire?

Usually a blinking check engine light is an indicator of constant misfires. I can think of a few things that could cause this. Pull the plug out of cylinder 3 and inspect it. If it is smashed or looks damaged you may have shattered a piston which will require an engine rebuild or possibly a new engine entirely. If it looks like it is in good shape screw it back in. The next thing I would look at is the spark plug wires and how recently they were changed. Usually it is a good idea to change them every time you install new plugs and make sure you use dielectric grease to ensure good connections.