What should I do to make my website 100% halal after having paid a deposit with haram money, and my desire to pay the remainder with halal money?

What is unlawful is not inherent in the money itself, but rather in one's responsibility (dhimmah). The unlawful money you have used is tied to your responsibility, and you must return it to its owners if they can be reached. Otherwise, spend it on the welfare of Muslims or give it to the poor and needy.