Fortune: Treasury Secretary Hank Paulson has careened from crisis to crisis lately, backing the Bear Stearns rescue, engineering the government takeover of Fannie Mae, refusing to commit taxpayer money to save Lehman Brothers, and Friday announcing a massive program to help banks offload mortgage-related assets. When he hasn’t been fighting fires, Paulson, the former chief executive of Goldman Sachs (GS, Fortune 500), and his team at Treasury have been working on two big, long-term issues that …