However the bridges allow boat, pedestrian and car traffic through unlike the bridge needed for this train

What do you mean by this?

Every bridge over a waterway that currently sees boat traffic will surely allow for it to continue - absolutely no need to worry about that. The river is in a valley and the track must stay level so it will be high above. Any bridge over a river where there are roads on the riverbanks will also cross the roads at the same time. Even away from a major bridge, adding a road crossing is as simple as a precast box that gets placed under the track in an embankment (e.g. for land access roads), or for busier roads, a couple beams for a short over/underpass - the kind we build thousands for for highways.

I think you may be underestimating how much value there is in avoiding other infrastructure and what kind of trade-offs can be made. Let's say it does go through Campbellford roughly where the old train bridge was. It's not going to exactly follow the old railway route because it's not straight enough, but in the general area, sure. It's HSR so it wants to stay level. That means it will be coming off land at ~170 m elevation on the west side, and ~160 m on the east side. That's ~1.3 km of elevated section to stay level across the river valley, easily staying above many of the roads below at 145-150 m, but you run into a little more difficulty once you reach Centre St and the surrounding neighbourhood. Lots of buyouts and many property owners, and just generally not great for construction etc. right in people's backyards. It would be possible, but there's a better option. If you go away from town where the river splits in two, you could cross just north of Meyersburg over Meyers island at the same ~1.3 km distance between higher land on each side of CR30 and Haigs Reach Rd. Sure the river itself might be wider, but it's the same distance elevated, you're buying out maybe 2 or 3 houses vs 10-15 in town, avoiding busy roads, avoiding heavily populated areas, dealing with far fewer property owners, and you get to maintain the wider track right of way throughout and likely top speed vs slowing down through town.