So *right now* the most serious problem for the order -- and for *all passenger railcar orders in the US* -- is the bankruptcy of Columbus Castings. This was the undercarriage / truck supplier for both CAF and Nippon Sharyo. This is the "supplier" who CAF vaguely refers to when saying that the contract will cost them $41 million dollars due to the bankruptcy of a supplier.
Amtrak will probably have to file with the FRA for another Buy America exemption for all future orders because there is no other maker of suitable parts in the US. Hopefully CAF has enough trucks for the order already made... because they can't get more.
Sadly, Columbus Castings is not just bankrupt, it's also shuttered:
http://www.dispatch.com/content/stories/business/2016/08/16/columbus-castings-sale-to-firm-that-wont-reopen-it-nears-approval.html
Frankly, I think Amtrak and some of the commuter rail agencies need to go in jointly and open their own company to produce railcar parts. Sort of like British Rail operating its own railcar factories. There's too much risk in outsourcing everything.