SAN FRANCISCO -- The overhaul of California's high-speed rail project could bring the Bay Area $1 billion to electrify Caltrain, and lay the path for bullet train service between San Francisco and San Jose sooner than anticipated.

The Chronicle has learned that officials with Bay Area transportation agencies are in negotiations with each other, and with the rail authority, to craft an agreement that would fund installation of an advanced train-control system, electrify the rails on the Peninsula and eliminate some of the rail crossings -- perhaps as soon as 2016, five to 10 years earlier than earlier estimates.

"There's a lot of work that needs to happen, and a lot of moving parts, but this is the closest we've been to seeing some real tangible benefit to Caltrain from the high-speed rail project," said Seamus Murphy, a Caltrain spokesman.

Proposition 1A, the $9.95 billion bond measure approved in 2008 that funded the high-speed rail project, would pay for the Caltrain improvements. But the Bay Area would have to match that money with a significant amount of local funds, perhaps as much as $1 billion. According to the plan, $600 millionwould come from bond money for high-speed rail service with another $400 million from bond funds dedicated to transit agencies proving connections to high-speed trains.

But there are still obstacles ahead. In addition to finding matching funds and proposing a package of improvements that would benefit Caltrain and high-speed rail, the Bay Area needs to convince the rail authority board to include the proposal in its business plan, which is expected to be passed in March, then hope the Legislature will release the bond money and include it in the state budget.

Dan Richard, a former BART director and new chairman of the rail authority board, confirmed discussions with Caltrain and Bay Area officials, and said it's an attempt to speed the plan to use commuter rail lines to help provide initial high-speed rail service.

"If we're going to come up the Peninsula on those lines, and use that right-of-way, then this would be advancing our investment in high-speed rail," said Richard, who was appointed to the board by Gov. Jerry Brown as part of an effort to overhaul the authority.

As part of that shakeup, the authority released a new draft of its business plan that bluntly acknowledged it could take 13 years longer than expected to build a fast train line between San Francisco and Southern California, and said it could cost $98 billion, more than twice the original estimate.

The draft plan also laid out a new phased approach, with the first stretch -- the so-called spine of the system where trains would reach speeds of 220 mph -- to be built starting this fall between Chowchilla and Bakersfield. The Central Valley segment would next be extended either to San Jose or the San Fernando Valley by 2021, and high-speed trains would start to run while the other end of the line is constructed by 2026. Until the commuter lines could be electrified, and tracks improved to accommodate high-speed rail, passengers would have to transfer to diesel trains to get to downtown San Francisco or Los Angeles.

But the authority is working in both the Bay Area and Southern California to accelerate improvements of the commuter railroads. Southern California officials have already agreed on a list of projects -- most of them eliminating or improving rail crossings or adding additional tracks -- and hope to get $1.3 billion from the high-speed rail bonds.