By JAMES GORDON MEEK WASHINGTON - Before he was captured last spring, Osama Bin Laden's top operational commander was solely focused on killing President Bush and Pakistani President Gen. Pervez Musharaff, the Daily News has learned. The capture last May of Al Qaeda's No. 3 leader, Abu Faraj Al-Libi, apparently thwarted plots to assassinate the two partners in the global war on terror, said a senior Pakistani official, whose information was corroborated by two senior U.S. counterterrorism officials. "Al-Libi had one mission: Kill Bush and Musharraf," the Pakistani official told The News. "He wanted to kill Bush in the White...