Internally balanced 340 questions

The water pump and timing cover have nothing to do with engine balance. Going by your photos, the engine has been rebalanced. The crank, balancer, and flywheel (looks correct for an internal balance engine) all look to have added fine balance holes drilled in them. Factory cast crank/external balance engines have different looking holes in the flywheel than what I see here. If all these parts came with the engine and from the machine shop who did the machine work, I would put it together and run it. If there is any question as to whether you have a matched set, I'd have the balance re-checked.