I'd recommend you have an electrician, or someone with very solid electrical skills, do the disconnect of the 2nd element. You've stressed safety all along the way with your research and changes and re-wiring water heaters is definitely not safe for someone to just get some advice and try themselves.
And, just once again tossing in my 2 cents, I wouldn't do it. You have a water heater, let it heat water, shut it off when you don't want hot water. You are concerned about legionella, yet you are proposing heating SOME of the water in the tank to a temp you think the water is all at and for a period of time you think is safe. Yet half that tank or more won't be at that temp, won't be at the same duration, due to disconnecting one element. Makes no sense to me.
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