I am not sure about the business class upgrade. Continental's site says Metroliner but that has offically been discontinued. Acela has replaced it (brought back briefly when Acela was down for break problems a couple of years ago).

I would not count on the Regional train with a business upgrade counting for onepass miles unless codeshared with CO as stated in their clause. The regional train, even with an upgrade, can be close to $100 less sometimes so they have little incentive to give a premium award. Even Amtrak offers only a standard reward structure (2 per dollar spent) for travel as oppose to Acela at 500 per one way.

Acela works just fine. I just go to the ticket counter instead of the machine and have them add my number. I seriously watch them type it though as it is EXTREMELY difficult to get them to get the miles after the fact. I've had to give up once or twice.