[ossiblue]

This is really a stumper. Is it possible that the new plugs have a different type connector nut on the top and (somehow) you are not getting the spark plug connector to seat solidly? It seems strange that only one side of plugs is misfiring. You said you had new wires but do you also have new end connectors? I assume you do and, if they're Beru, be sure you get that clear "click" when the connector seats properly--either by sound or feel. If you're certain all 6 plugs are solidly connected and the problem persists, then I'm out of guesses.
Good luck and keep us updated.