SANDAG has been working with NCTD & others for several years to connect sidings and upgrade to 2 main line for several years. Might want to check their web site for more information.
NCTD might have something at their web site too in the way of current projects. If nothing else, the projects show up in the TIP, and Google Maps have been showing the work fairly well. I think the Train Simulator territory for the Surf Line needs updating ...
Money for hooking together sidings has been fairly easy to come by, especially with the I-5 widening project coming on line (mitigation money etc.). Money to replace & widen bridges has been a little harder to get, but some have been done. Of course, doing something serious about the Miramar Grade will cost real money.
All that is about SD County. On the Metrolink side of the line (north of San Onofre) things are a little less clear.