Now that the California High-Speed Rail Authority has met an Oct. 2 deadline to apply for a portion of the $8 billion set aside for high-speed train development under the American Recovery and Reinvestment Act, lots of other stuff is going on that threatens a 2012 construction start, at least in Northern California.

The authority’s board recently approved an application for more than $4.5 billion in federal stimulus funding for engineering, design and construction on the state’s high-speed train system – generating an investment of $9.1 billion when state matching funds (Prop 1A, passed last November) are added.

Included in the authority’s projects list is a request for $400 million in ARRA funds for the construction of a new Transbay Terminal in San Francisco, which is, according to the authority and the Transbay Joint Powers Authority, which oversees the new transit center, the preferred site for the city’s high-speed rail terminus.

While all this stimulus applying was going on, the state’s attorney general’s office responded to a letter sent to it by the TJPA attorneys that asserts it is “legally improper” for the authority and the Federal Railroad Administration to analyze any alternatives to the Transbay Terminal.

What got this contention going in the first place is pretty sketchy. There has been at least 10 years of public comment and scoping, environmental reviews and board meetings, so the two alternatives often cited would have had to be brought up at some point. The authority would have had to study these and make a recommendation (which it did).

These two sites -- the current Caltrain station at Fourth and King streets and a three-block area adjacent to the new terminal site at Beale, Main, Mission and Howard streets – have good attributes and not-so-good ones, just like the Transbay Terminal. All we know is Arthur Gensler is in favor of the Beale site, according to a recent letter from Christine Sproul, deputy attorney general, to Mehdi Morshed, executive director of the authority.

What probably goaded the opposition to the Transit Center terminus plan was San Francisco Mayor Gavin Newsom’s comment, after viewing the French high-speed rail system (TGV) in late January of this year, that the state’s high-speed rail system must terminate in the new Transbay Terminal in downtown and that a “train box” be part of that project. This train box, he says, would handle the HSR trains as well as an extension of Caltrain.

And then he says, “We should not spend $2 billion to build a glorified bus station.”

Bravo, Mr. Mayor, way to dis buses.

Many people will actively reject the time, cost, dust and inconvenience of digging a big hole at First and Mission, but, as the mayor says, you should want the system to stop where the surface transportation is prevalent and within walking distance to major downtown businesses.

But also throw in the fact that the first set of designs by Pelli Clarke Pelli does not include a train box. Methinks more design delays are forthcoming.

Then a couple of weeks ago, a new entity, the Peninsula Cities Consortium, which includes the cities of Palo Alto, Menlo Park, Atherton, Burlingame and Belmont, is saying that the authority better make sure that community voices are represented in the planning stages.

The HST tracks will parallel the Caltrain tracks down the peninsula to San Jose. In order to keep somewhat high speeds (around 120 mph; its top speed will be 220 mph), the consortium says it fears the authority will make important decisions on right-of-way issues on ground-level tracks and options of tunneling and raised overpasses without the cities’ input. This will probably result in endless EIR meetings.

Anyway, this is just the tip of the high-speed rail iceberg. Many more obstacles are projected. Anyone venture to bet that our brethren in Southern California will be the first with the shovel?