All those crossings are going to have to go eventually, anyway, aren't they?
I'm still not sure why the 3 at New London are nearly impossible to eliminate, either. You've already got some awful speed penalties coming your way from that S-Curve, adding a 1% or even a 0.5% grade to jack the tracks up about 10 feet isn't going to hurt you any worse. The curve is already complicating (read: raising the price on) matters on making those platforms high-level, and they're going to have to be high-leveled because M8s can't do low-platform boarding. No matter what, something needs to happen to the grade crossing at the station itself: at present, there's literally no way to cross the tracks once the gates come down. You're on the wrong platform for your train? You just missed it, sorry!
Here,
this is what I came up with. Added bonus? +16' 9" to clearance at Shaw's Cove, which might get the Marine Trade NIMBY's to actually shut up when combined with the higher clearances on the reconstructed CONN/NAN bridges.
Speaking of movable bridges, it's a nice starting point for if the bridge over the Thames River ever gets elevated to the same height as I-95.