One cylinder out of six will kill your power, so I doubt there is a problem with two. I don't think you would get around the block on four.

If it's knocking at idle, the thing to do is loosen each line with the engine running. If you're careful about not letting foreign objects go into the engine, you can run it without the crossover pipe in place.

I would find the cylinder that isn't firing properly, and remove the delivery valve again. Get another new O-ring and seal and put it back together. Perhaps the spring is out of place now.