Lake,
Good research, good read, good write up. It is great that there are living connections to Jax history like this.
I agree with Stephen, how could such a great legacy built up by the city fathers be left to rot?
On the flip side, dredging McCoy's Creek based on what you have written here would no doubt pull up some undesirable stuff, probably worthy of federal scrutiny.
This might explain some of the collective civic ignorance from Stockton Street all the way to the St John's. Keep people away from the risks and try to let nature resolve it. Unfortunately some of the compounds used back then (lead, phosphates, creosote) can't go away naturally, it would have to be removed.