The current Tremont St. tunnel portal is intact underneath the
front walkway of the day care center building, underneath those fenced-in trees. This is what it used to look like before the park was filled in on top of it:
Emerged below street level in a pit with the 4 tracks hugging each side of the block. Block's been reconfigured in the years since with Charles St. Ext. on the left reshaped, turning this block into a wider trapezoid instead of narrow triangle. All buildings except for the condemned church are behind the portal, so all this ex-incline space is there for the taking.
The Tufts station would basically remake this track layout verbatim with slightly wider wedge in the middle. Shallow depth, sort of like Boylston St. station with no buildings on top except for the headhouse coming out of the center. Your triangular wedge platform touches the 2 inner tracks, and there would be side platforms grafted onto the outer tracks. As mentioned, probably will have an underpass connecting them all...and that's also where you would snake the ped tunnel across the Tremont-Washington block to reach the Orange Line (probably pointing NW from under the platforms and traveling under the parking lot next to the Tufts garage to reach the OL).
The wye track would go the length of the south end of the park. From the angle in that historic picture, you would basically be standing on the outer wye platform as you point your camera.
So...the tracks to the right of the picture are the old City Point branch. That's your trajectory for the Seaport and Washington. 1 block of tunneling underneath Shawmut to Marginal St. The Orange Line tunnel basically splits the Quincy School building down the middle at the corner of Shawmut/Marginal and crosses the intersection at an angle. So you would have to have a pretty steep incline (no big deal for a trolley) on this block to dip under the tunnel and structurally underpin it. Higher difficulty, but not infeasible when the area of impact is confined to 100 sq. feet under an urban renewal intersection with the school building's foundation safely set back from the corner. Helluva lot easier to square than what SL Phase III attempted (and ultimately failed) to do underpinning all of Boylston and Chinatown stations with BRT tunnels and stations under impossibly narrow Essex St.
The Seaport tunnel would diverge here and curve under Marginal St. hugging the Pike retaining wall (probably inclining up to a little shallower depth in the process). The Washington St. tunnel would diverge at the same spot and go diagonal underneath the Pike and NEC while inclining up. The portal would go
here along the Herald St. retaining wall where those electrical boxes are on the side of the NEC, with the incline to street level grafted onto the Herald wall. This is the space formerly occupied by the Boston Herald's freight siding; you can see from the way the NEC tracks curve around it 2 blocks east and 2 blocks west that this was a siding and not a thru track, so that space will never be needed for RR operations. Hit the street at the Washington/Herald intersection, graft a trolley signal phase onto the traffic light, and hang a right down Washington.
Back at Tufts station the Back Bay-->Huntington tunnel would take the former Egleston Branch tracks on the left side of the historic photo. Then a 1-block tunnel down Tremont to Marginal, then curve onto Marginal westbound. Follow Marginal, Cortes and the Pike retaining wall to Clarendon St. Then cross underneath the BBY garage's circular car ramps and hug Trinity Pl. to the Stuart-Huntington block...always staying to the north side of the covered-over Pike retaining wall. Tight squeeze here, but the only building impacts are those circular garage ramps. If anything has to get underpinned or wrecked/rebuilt, let it be those and not any buildings themselves. BBY station's Green platforms would be well offset from the rest of the station, so your connecting walkway would go somewhere through the ground level of the garage under or behind the Dartmouth St.-facing retail side of the building. The Huntington tunnel joins at the corner of Exeter/Stuart/Huntington under the Shaws front lobby (saving you from having to cross the Pike).
The wye tracks obviously let you go straight through from the Seaport to BBY and Huntington.
The only movement that's impossible with the tunnel configurations out of here is Washington-->Seaport because of the angle and depth at which those 2 tunnels coverge @ Marginal/Shawmut. But that was one of the main criticisms of the conjoined Silver Line: Roxbury-Seaport is too low a demand thru route that nearly all ridership from either end would transfer out downtown and not ride it end-to-end. No big loss. And if you want path-of-least-resistance tunneling you have to accept some non-critical compromises like this. I don't think Dudley Sq. is going to protest when they can wait on the Tufts platform and ping right back out to the Seaport.