As a Springfield area resident, I can confirm that all the 400-series trains to/from New Haven are 2 car coach only trains...no BC, no cafe. So get your coffee before boarding. The Valley Flyer's are simply an extension of those trains to Greenfield. At New Haven, you'll be switching to either a NEC regional train or an Acela. Both have upgrade capabilities to BC on the regional, or FC on the Acela.
Traveling alone, I've used upgrades to FC on an Acela a good number of times. For what it's worth, I have NEVER had success using the Amtrak web site or the Android Amtrak app to do an upgrade. I've even tried using Edge instead of Firefox and get the same results. I've ended up calling and then letting them assign a 'default' seat. It seems that many of the agents don't know how to select a specific seat. I then go back online and change the seat assignment to what I want.
And using companion coupons? What a nightmare! The AGR portion of the Amtrak site shows instructions of how to do it, none of which work! It should be an on-screen option/button while booking!
Just this past Sunday, I booked a trip for me and a friend on a one-day, 4 leg 'circle' tour starting and ending in Windsor Locks CT. Hopefully, we'll see some good fall colors on the WNL-NYP-ALB-SPG-WNL trip, especially along the Hudson next week. I called and the person I talked with asked for specific coupon numbers (you have GOT to be kidding!) even before I was asked for my AGR number! I told her that once she had my number, it should be easy to click on my coupons and apply them. Her response was that she does not have that capability on her screen! AGR contractor operation, I presume? She managed to get the trip booked for 2 people, but no application of companion coupons (I read the 1st one 3 times and she got it wrong every time!) nor was my AGR number shown. I had to call back Monday morning to talk with someone who applied the companion coupons in less than 5 minutes! I didn't realize my AGR number was missing until after I printed out the tickets. I figure I'll have to go through the 'missing points' routine a week or so after we travel.
On one trip, a couple months ago, my friend and I took a 400 train to NHV and then an Acela to BOS, then #449 back to SPG using 3 companion coupons again. Trying to change BC seats on the Acela on the web site was impossible as it was for 2 passengers. I called and spent a good 10 minutes telling the agent repeatedly I wanted seats together on the right side of the train to get ocean views while traveling. The agent finally figured out what I was asking and to our dismay, they were on the LEFT side! Fortunately, when the conductor came through, he managed to move us to a table in the front of the car with both of us facing forward.
Hopefully, using upgrades for you won't turn into a horror story like my experiences. And, as an aside, one cannot upgrade when using companion fares...as in 'been there, tried it'.