Luckily the Welland Canal bridge already has a decent amount of elevation over the Welland Canal due to it being on the escarpment edge and adjacent to a lock (quick measurement appears to be about 12m of clearance).
Maximum ship height on the Canal is 35.5m, so assuming we give an extra few metres of height (say 38m, which seems to align with other bridges) we would need to elevate the existing bridge by about an additional 26 metres in height. That would still require a pretty significant structure, especially on the west side of the Canal where the rail lines already slop up towards the Canal, but wouldn't be as significant as you may think.
There is space to berm most of the grade change as well from a quick glance, which should reduce costs.
Still going to be hundreds of millions of dollars, but at quick glance the project wouldn't be too much larger than the Davenport Diamond project, if anything likely a similar cost point given a less constrained construction environment and likely far less structure involved.
The Davenport Diamond contract was $175 million, for comparison.