When President Clinton and Defense Secretary Les Aspin finally get around to filling second-tier jobs at the Pentagon, the appointees will be plunged into a raging internal battle over Star Wars. The big problem is that the $3.8 billion allocated for the Strategic Defense Initiative isn't enough to fund its big projects. The only major program that seems safe in the post-cold-war world is a tactical anti-missile system designed to protect troops from attack. This follow-on to Raytheon Co.'s Patriot system would be useful in regional conflicts like the Persian Gulf war. Left scrambling: funding for research into basic technologies, such as diamond films, and development of a system to protect the U.S. against strategic-missile attack. The Administration's preliminary budget hasn't made choices among these competing programs. "Until the new Clinton cadre gets in, we'll have internecine warfare," says one top Pentagon official.