Here is a possible solution to the problem of the new Interstate 5 bridge not being high enough to accommodate some river traffic. I am not in favor of light rail, but if it has to be, maybe it could be put on a bridge with a lift, maybe the newer one of the two that are there now.
With as few bridge lifts as there are now, it seems like 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.
It seems like there is 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 and not have to worry about it being too steep for light rail.
The new bridge or bridges also should be built as close as possible to the existing spans, preferably on the upstream (east) side to keep them as short as possible, keeping the costs down and hopefully eliminating the need for tolls.