John A. Thain, the new chief executive of Merrill Lynch, is set to receive an initial pay package of nearly $50 million as he embarks on a quest to restore the firm's reputation and risk management practices after a devastating few quarters of subprime and credit losses. The pay package is largely composed of stock and options that could be worth more than $120 million if MER stock rises more than $40 a share in the next two years. The pay, disclosed in a regulatory filing today, will make the executive one of the highest paid on Wall Street. It is also three times what he earned over his first three years running the New York Stock Exchange and may approach the pay level of hedge fund traders and top executives at Goldman Sachs, where Thain previously worked.