The delay could affect much more than funding for the project (and as the article notes, FTA is sufficiently "invested" in the project that they're likely to do more than grumble). Talk to your friendly planning staff at SCAG. If delayed completion of a major project like that passes certain dates, it can affect the "SIP conformity" status of the whole Regional Transportation Plan (or at least the South Coast AQMD part of it), delaying a lot more than just that one project. Ask Sacramento, which got hit with a similar (though a lot smaller, obviously) issue with building light rail in olde downtown streets.