California Line: the CL is a simple linear line comprising of the most used stops. Starting in San Diego (this could even be supplemented in the future with a Tijuana stop if things work out) the route goes to Oceanside, Huntington Beach, downtown LA, then Oxnard. Not only will this route provide overland transportation but it could even act in a rough commuter sense, ferrying people from Oxnard and Orange County to downtown. There is a long stretch from Oxnard to Salinas and was chosen primarily for scenery as most SF-LA travelers would presumably be on vacations. I'm not sure of the make up of the average passenger, if they would be vacationers or business but this route can easily be supplemented with a more utilitarian route though the valley to Bakersfield and Fresno. Whatever the route, the rail passes through the Bay Area with stops in San Jose, San Francisco, and Oakland. Perhaps even a stop at Berkley to supplement the college crowd which I will touch on later. The route finalizes with passage through Stockton and the capital of Sacramento. To augment profitability (which is the key in all of this), the route ends at Reno-Lake Tahoe.
LA-Vegas Line: Arguably the biggest cash cow in the whole deal. A simple low cost straight (or as straight as possible) line from Los Angeles station to Las Vegas. As TheMann pointed out, this could actually be augmented with another straight line from Vegas to Phoenix. Not only would this provide another cash link, it would indirectly link Phoenix and the California line, thus furthering the high speed link.