Many moons ago I worked with a guy that had been on the XB-70 project at North American. According to him, the popular theory was that the F104 got caught in the wing vortex of the XB-70 which flung the F104 into the vertical stabs (the collision took out both the vertical stabs on the XB-70 making it uncontrollable and it went into a flat spin).
Supposedly there is some spectacular video of the collision (after all, it was a photo shoot) but most of it remains classified.