Crossings shouldn't be a problem. As for "public" crossings, I can think of the one at the north end of the marina, the Haddam Meadows crossing, and Landing Road in Higganum. I could see them all being "just crossbuck/stop signs" initially. Perhaps the Haddam Meadows crossing would be first to get an upgrade as it is the main entrance to a state park.
Let's not forget that it's not 100% solved once you get to Maromas. You've still got 5 miles of track to cover before you reach the diamond in Middletown. Granted, that's P&W property (right?) / controlled. And some of that track was rehabbed some 15-20 years ago (at least), and hasn't seen a train in quite some time. There were some washouts along that stretch last time I knew, and some bridges that probably need work. It's been some time since a train headed down to Pratt & Whitney, and since the end of the sewage trains, they haven't gone south of downtown in awhile, as far as I know. Plus, doesn't the city/state still have the line ripped up along deKoven Drive for the pipeline? Or at least it did a month or two ago. There's probably just no reason for P&W to head any further south on the Valley line than they have to, but given the right circumstances, I'm sure they could put their portion of the Valley back together.