Really stupid question, you do have the plug leads in the right order?????
I'd be pulling the rocker cover to recheck if the valves are opening, and if they are, opening when they should be. Whip out the plugs and earth them to the block. Crank the engine to see if each plug is actually firing.
Had an issue like this with aftermarket leads. Was misfiring on a couple. Put standard leads back on and all was sweet. But the red ones looked so good...... :sob: