Here is a possible solution to the problem of the new I-5 Bridge not being high enough to give enough clearance for the river traffic.
I am not in favor of light rail, but if it has to be, maybe it could be put on a lift bridge, maybe the newer one that is there now.
With as few bridge lifts as there are now, perhaps that could work, especially if the opening of the railroad bridge was brought into line with the high part of the bridge that the boats go under.
There seems to be enough notice of a bridge lift coming to substitute a bus or two for the train if necessary. This way, the height of the new bridge could be as high as necessary to accommodate all possible river traffic without having to worry about it being too steep for light rail.