My bad...I forgot to explain where I was envisioning the rail line would enter/exit the highway median in my earlier post.
On the Providence end, I was picturing it would curve out of the median just before the state line (i.e. where the median ends) and then shoot northwest, pretty much directly along the state line, up to Route 44. Then it would turn west and enter the intact-but-mostly-unused Henderson Expressway right-of-way. It would follow that to the Seekonk River, where it would cross via a new bridge (the one Crook Point Bridge would have to be replaced even if you wanted to use the historic alignment) and then enter the tunnel.
This alignment would likely have a small handful of property takings, but they would be industrial or commercial rather than residential, which should make the land acquisition process less contentious. There would be one or two crossings of the Runnins River right near the highway; if bridges aren't good enough for environmental regulators, maybe that short segment gets built as a trestle. The curves through East Providence would slow trains down enough that it probably makes sense to add a station here.
View attachment 67533
On the New Bedford end (which you only need to worry about for the version of this idea that includes a through connection to the Cape), I imagined the transition from the Watuppa Branch to the 195 corridor would occur on the northern half of the interchange between 195 and JFK Memorial Highway, which might require moving away from a cloverleaf design for those on-ramps (or at least reworking their clearances as needed).
I acknowledge that the buildings fronting on Cedar Grove Street are probably too close to escape unscathed even if you ran the rail line directly against the northern side of the highway. Besides that, I don't see any other obviously-necessary takings; 195 has a median on the Fairhaven side of the river, so you'd want to get the rail alignment back into it as soon as practically possible.
This alignment doesn't hit the existing station, so another New Bedford station would have to be established for this line. Maybe the vacant site off Hathaway Road in the top-left corner of the image below would be a viable option. The track is straight and there's plenty of space for parking and ideally some TOD.
View attachment 67534