For two decades, the project lay dormant due to lack of funding until Caltrain agreed to share its tracks with the CHSRA, which was looking for a route for the legally mandated San Jose–San Francisco segment.

[6] By 1977, Southern Pacific were facing rapidly declining ridership and petitioned the state Public Utilities Commission to allow them to discontinue the commuter rail operation.

[9] The primary benefits of an electrified railway would be improvements in air quality, noise, and acceleration, but would also save on other ancillary costs, such as lubricating oil, cooling water, maintenance, and refueling.

[9] The 1992 Feasibility Study recommended the use of electric locomotives and 25 kV AC overhead lines as the most cost-effective alternative, since the gallery cars, which had been built in 1985, were then relatively new and could be reused.

In 1997, Mayor Willie Brown canceled the appropriation for San Francisco's share of costs to extend rail service to downtown, saying Peninsula residents "ought to fund the whole project" since it would mainly benefit their commute.

Mike Nevin, PCJPB member from San Mateo County noted that while the downtown extension "would have enhanced particularly the electrification of the system", lack of it would not cause Caltrain to collapse.

Steve Schmidt, a councilman from Menlo Park, argued that electrification instead should be the top priority to make the rail line more palatable to neighbors, citing improvements in noise and pollution.

[19] Despite increasing ridership, Caltrain experienced a budget crisis in 2011 that nearly forced it to cut service to peak commute hours only,[20] while funding sources for electrification remained unidentified.

[25] In March 2012, Caltrain and other local agencies signed a memorandum of understanding with the CHSRA that detailed the blended plan,[26][27] which received approval from the Metropolitan Transportation Commission a week later.

[28] Under the memorandum, $706 million from the high-speed rail bond would be matched by state, regional, and local transportation funds to pay for the estimated $1.5 billion needed for CalMod.

Residents opposed electrification and the proposed high-speed rail route because the overhead electrical lines would require tree removal and the town could potentially be divided in two by permanently closing the two grade crossings at Fair Oaks Lane and Watkins Avenue.

[34] In July 2015, the suit proceeded after Caltrain's request to the Surface Transportation Board to exempt it from California Environmental Quality Act (CEQA) guidelines was denied.

Atherton reiterated its opposition to electrification on the basis that overhead wires would require removing a significant number of heritage trees, and city representatives asserted that "newer, cleaner, more efficient diesel trains" should supplant plans for "century-old catenary electrical line technology".

[37][38] Indeed, at bottom [California High-Speed Rail] is providing funds to Caltrain while hoping that the rest of CHSRA's plans work out well enough that, someday, it can bring the blended system to fruition.

[52] In April 2016, after missing the initial October 2015 deadline, Caltrain requested a third party review of the CBOSS project from the American Public Transportation Association (APTA).

[58] In early 2016, the CHSRA had selected a route that required extensive and costly tunneling in Southern California and revised its initial operating plans for high-speed rail to include the Bay Area.

[62][63] However, during the review period, the fourteen Republican party U.S. House representatives from California sent a letter to Secretary Chao, urging her to deny funding due to the project's ties with high-speed rail, which they opposed.

[66] Another Republican signatory, Representative Devin Nunes, was unmoved by arguments on infrastructure benefits, saying in late February that he would not "feel too bad about one of the richest places on the planet not having a train.

"[67] Fellow Republican Representative Jeff Denham defended the letter, saying Caltrain's electrification project and CHSRA were closely intertwined because the former derived some funding under the "blended plan" agreement.

[68] Representative Mimi Walters also made a statement that she was not opposed to electrification, but instead held "serious concerns about the use of taxpayer funds for a project that is tied to high speed rail".

[62][75] Under the preliminary budget proposal released in mid-March 2017, the United States Department of Transportation's Capital Investment Grant Program would be eliminated, although approved projects would continue to be funded.

"[78] Henry Grabar noted the grant deferral could be "an early test of a simmering fear that the state's outspoken political opposition to the Trump administration might come with a price".

[69] San Jose Mayor Sam Liccardo met with Department of Transportation officials, urging them to upgrade a system that "was built under the presidency of Abraham Lincoln".

[80] On April 30, legislators in the U.S. Congress released the proposed 2017 federal budget, which included partial funding for the electrification project, but restricts its distribution unless Secretary Chao signs off on the grant.

Key decisions in the development of CalMod can be traced back to the 1992 Feasibility Study, which recommended 25 kV AC overhead lines;[11] the 1998 Rapid Rail Study, which recommended low-cost upgrades to first improve service and build demand;[17] the 2006 Caltrain 2025 proposal, which proposed the use of lightweight electric multiple units;[130] the 2009 FRA waiver, which imposed certain conditions on mixed traffic;[131] and the 2012 memorandum of understanding with CHSRA, which resulted in a "blended" system to use the existing twin-track line as much as possible.

[160]: 3.4-19 to -21  The tunnel notching work was performed during weekends, so service between Bayshore and 4th and King was replaced by buses starting on October 6, 2018, with a planned "late Spring 2019" resumption.

In addition, a rolling maintenance platform was added to the building to allow work on the top of the train cars, and a permanent tent was erected for parts storage.

[162][163] As a result of the blended plan, PCJPB mandated that Peninsula Corridor infrastructure and equipment should be compatible with future California High-Speed Rail Authority (CHSRA) trains.

[178] In January 2018, PCJPB applied for $631.5 million in state funds for the Electrification Expansion Project (EEP), part of which would be used to exercise the option to purchase an additional 96 EMUs at a cost of $600M.

[189] As of January 2019[update], an option has been exercised to expand the order to 133 cars using Transit and Intercity Rail Capital Program funding, to be delivered as 19 trainsets, each consisting of 7 railcars.