Check each of your spark plugs for signs of rust or any indication of water in the cylinders. Also look for any differences. Sometimes water can leak into the cylinder during the down stroke after changing a head gasket. Have you done the final torque down yet. Check your ignition - spark plug cables... and make sure the gap didn't get messed up on any of the plugs while you had things apart.
The timing would still be the most obvious possibility and I doubt it's a fuel issue.