Interleaving into the flow on the Stouffville line (which is planned to absorb a ginormous volume of closely-spaced RER trains) will be complicated enough over the short stretch from the CP overpass down to Kennedy and on to Scarborough Jct. Joining the line further north, and having to follow GO trains that will be stopping all the way down, would be very painful.
Exactly. I think VIA north of Agincourt would be a nightmare, given the narrow right-of-way, totally different stopping patterns, lack of grade-separation, tight curves, and lack of space for grade separations or curve widening.
I don't think it would be much of a big deal south of Agincourt though. There are no intermediate stations between the CP line and Kennedy, and if they do build Lawrence East station there will be enough room for a third and maybe fourth track in the station itself, allowing fast trains to overtake stopped locals if necessary. Kennedy itself is such a massive hub that I figure that most if not all VIA trains would stop there. And Metrolinx is already planning to grade-separate Scarborough Junction and quad-track the Kingston sub from there to the USRC, so express trains can overtake the frequent local services at Danforth and East Harbour.
There is now plenty of room to build a dedicated main line track for HFR skirting along the north side of the Agincourt Yard. It will be interesting to see how a connecting track would be built to reach the Stouffville line. Curvature will be tight, which means trains will have to run slowly. Ideally one would have an underpass under the CP line, but that's expensive and could take time to build. If the connecting track isn't an underpass, it will have to cross CP's freight line at grade, similar to how VIA transits Smiths Falls at the moment. That's a recipe for CP to undermine the whole premise of improving reliability by removing conflict with freight...... doubly so if VIA intends to carry on along the Belleville Sub to Leaside and down the Don Branch. And if VIA does choose the GO line, trains will cross over at grade to join that line....inevitably this will conflict with GO movements. All doable, but the useable high speed portion of the line will likely end around Tapscott.
I think the travel times would be similar whether VIA runs via the Don Branch or the Stouffville Line. Either option has several slow segments.
Here's how I had envisioned the Stouffville Line option:
Due to the huge height difference between the CP and GO lines at Agincourt, it wouldn't be possible for the VIA line to cross over both at once. So VIA would need to run on the south side of the CP corridor. The initial HFR project could work with single-track operation along the eastbound curve, but I think there's room to future-proof for a separate overpass for westbound VIA services to resolve the conflict with northbound GO trains.
The next three road crossings (Midland, Sheppard, and Brimley) have 5-track overpasses, which leaves room for 3 tracks for CP (or 4 if VIA only uses 1 track).
Then the right of way conveniently widens, which would make room for a ramp leading up to an elevated structure bringing VIA over the CP lines and McCowan Rd.
Like you said, it shouldn't be a problem to carve a ROW out of the west side of the CP yard, since any lost tracks could be replaced using the giant empty space where the hump yard used to be.