You might write to Amtrak headquarters (National Railroad Passenger Corporation, 60 Massachusetts Avenue, N.E., Washington, D.C. 20002) and complain. Remind them that the the delay exceeded by several times the total amount of time you'd planned to spend completing your journey, and the apparent cause was Amtrak's own defective equipment.

Reading between the lines on http://twitter.com/PACSurfliners and elsewhere, a dragging wheel on an earlier Amtrak train required Metrolink and NCTD, who own the tracks Amtrak uses, to call out track inspectors to look for damage before train traffic could resume.

Be sure to include your ticket or reservation number (or a copy of your ticket stub) in your letter; I understand they're usually pretty good about providing some kind of adjustment after the fact.