Friedo is right, but it gets much more complicated. Railroad timetabling is one of the black arts.
On the suburban rail network here in Sydney, an electric commuter train will need an additional minute added to the timetable for each extra station it must stop at. “Dwell time” (stopped at station) is only about ten to fifteen seconds of this. The rest of that time is due to braking and acceleration.
Your Californian line sounds like a hybrid system that is running commuters, intercity, freights, you name it. This mixing of different train types is a major headache for timetabling, and is avoided as much as possible in the construction of new railroads. If you look at the cities with dedicated “metro” type commuter networks, you will see that they make very good headways, with the trains running very close together - often only a minute or so apart. They can do this because the signalling system (as described by friedo) is built around a single type of train - and that train is light, and capable of wickedly good acceleraton and deceleration. These trains can get closer together safely. Start putting freighters into the mix - even if it’s only one or two a day - and you need to rejig the whole signalling system. The block sections get much longer to allow the driver of a 3000 ton freight to pull up if he suddenly gets a red signal. Thus the freights become the weakest link, and all other trains must now adapt to them.
Dwell time itself is a whole 'nother kettle of fish. Metro and subway trains are designed for quick dwell times, at the expense of other things such as passenger comfort. These trains have two (or often three) very wide doors. Often up to half the side of the train is made up of open doors when you see one of these at a station. They can transfer people between the train and the platform at a high rate. All this extra space devoted to doors means fewer seats. In many systems, there are only longitudinal seats (to keep the inside of the car open plan for quick passenger movement). Even fewer seating positions! Now, on an intercity train, you don’t want to be standing for two hours, so those cars will tend to have small doors at the end, and comfortable lateral seating. This can involve a jumbo jet type of queue appearing in the aisle as people wait to get out at the station. In addition, people on these routes are trying to manhandle bulky luggage whereas the downtown commuters are not. Then there are things you wouldn’t even consider: how long is the roof on the platform? Does it run the full length of the platform, or is it a mean little forty foot long affair in the middle? If the latter, watch what happens on a wet day. Waiting passengers will crowd in one spot. When the train arrives, they will all attempt to get into the same one or two cars, resulting in queuing. Do last minute people try to run at the closing doors? There’s another ten seconds wasted as the conductor must repeat the whole procedure of giving the engineer the all clear. All this stuff has a significant effect on timetabling when multiplied by the number of stops.
You may find that the actual line speed limits are lower than they were in the 70s. Maybe funding cuts have made the line substandard and there are speed restrictions on certain sections. Here in Sydney, the speed limit over switches has been drastically cut. Not because the trains can’t handle the former higher speed with absolutely no danger of derailment, but because these days people are more likely to sue, and passengers being jostled on Sydney trains have done just that. This also applies to hard acceleration and braking. Engineers used to do this to make up time (or to keep to unrealistic timetables), and now they are scared to. They used to creep up over the speed limit a bit to, but no more. There are actually passengers who use GPS equipment to see if the engineer is speeding, and will then report him. The railroad companies themselves use police style lineside radar to catch speeding trains. They are too scared of their insurance premiums now. As you are in California, the litigation side of it is probably even worse.
The insurance and litigation side is almost definitely a factor. The technical stuff I mentioned earlier may be, but I don’t know what the situation was in the 70s compared to now. Some things may have changed either way, others probably haven’t. They are definitely variables to consider though. Timetabling is a very, very complex thing.
I would say the