Extra passing tracks have been added, nearly doubling the amount of track that needs to be electrified. This is to support Baby Bullet and the California High Speed Rail effort. At $2M per mile of double track and 77 miles of track, that's nearly another $154M .
When the initial $376M budget was made, there were only 60 daily trains. Today there are 80 daily trains, and by 2003 there will be 110 daily trains. Extra equipment will be needed for the electrification effore. Additionally, it's highly likely that Electric Multiple Units may have be chosen. At $150M to replace 70 cars, a 120 car fleet might cost an additional $120M.
Perhaps the best reason there's a budget increase, is that the California High Speed Rail Authority has offered to pay 50% of the electrification costs. Curious how the budget suddenly zooms 40% higher!
Here are my numbers:
$154M (extra track) + $120M (extra cars) = $264M
$376M (original estimate) + $264M (extra track/cars) = $640M which is pretty close