As I understand it you can earn miles on amtrak in two ways:

(1) Flight on CO to EWR and then connecting on any Amtrak train with scheduled service to New Haven, Stanford, Wilmington, or 30th St.

(2) An Acela train segment between New York Penn and Washington or Boston. As I read it, that segment has to originate in New York.

Thus, as noted above, your itin. does not appear to qualify. See: Amtrak Partner Rules

No longer Metroliner on NE Corridor. Acela classes are business class and first class. Non-Acela classes are coach class and business class.