As you've disturbed the plug caps I think it might be worth unscrewing them and trimming the HT leads by enough so that when you screw the plug caps back on they are going into fresh lead, the ends are known to deteriorate over time and not connect properly, so this could fix your problem.
If the two cylinders that are not firing are being fed by the same coil you might need to check / clean the connections etc.
If the two cylinders that are not firing are being fed by the same coil you might need to check / clean the connections etc.