According the the response Amtrak is further along than the freight railroads are with the I-ETMS (Interoperable-Electronic Train Management System) which will be used by both Amtrak and the freight railroads. There is a suggestion the FRA will have to request an extension of the deadline on behalf of the freight railroads and that this should also give Amtrak the time it needs.
AMTRAK's OIG has issued a report stating that it may not be possible for AMTRAK to meet the PTC deadline. Many of the items will also apply to freight RRs. Problems are including lack of radio spectrum, inoperation, and others. Here is the report ----------
http://www.amtrakoig.gov/sites/default/files/reports/amtrak_oig-e-2013-003.pdf
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