If Company A is 30% equity, 70% debt currently, but will have a capital structure of 50% equity, 50% debt in year 5, which capital structure do you use for your DCF?

The 50/50% capital structure would be used. When calculating WACC, we assume the target capital structure, which is the capital structure the company will have in the long term. This is because the value of a company is determined by its future cash flows, and not its current cash flows, so the long-term capital structure is much more relevant.