Elevating a light rail Urban Ring line over the Grand Junction railroad could still be done, even with the MIT building. The line could ramp down to surface level at the MIT building, then up again, and also ramp down at other locations where the Grand Junction ROW is wide enough to accomodate the two tracks of light rail, while still leaving room for the railroad. The line would really only have to be elevated at street crossings. The elevated line route could either go through East Cambridge on the Grand Junction, elevated over the Cambridge St. crossing, or instead leave the Grand Junction RR at Binney Steet, following it to Land Blvd., then above Land Blvd. up to Lechmere Sta.
Such a route would also allow one or more of the Green lines (B, C, or D) to use this Urban Ring route through Cambridge, and then enter downtown via the Lechmere viaduct and Science Park. This would relieve congestion in the mainline tunnel of the Green line in the Back Bay and downtown.
I would also propose for the Urban Ring a light rail bridge over the Charles River, parallel to and on the east side of the BU bridge. There is enough horizontal clearance between the BU bridge and the nearest BU building to allow an elevated light rail line there. The light rail bridge would basically be at the same elevation as the BU bridge, so the visual impact would be minimal. The elevated line could then pass over the Comm Ave/BU bridge intersection and parallel the Mass Pike for a little ways towards the Fenway area. It would be a lot cheaper than tunneling under the Charles River.
Bus-only lanes for the Urban Ring are a terrible idea. Light rail, located on elevated sections in congested areas and where ROW is available, would provide rapid transit unavailable from a bus system, plus give flexibility in routing the Green line.