I don't know if I can answer all your questions, but I can definitely answer the most important one, so you can quit twitching! LOL!
spoiler:The hidden room is in Warehouse #2, which belongs to the Dockmaster. Enter the warehouse, go up the stairs, through the double metal doors on the south side, down the hall and into the last room on the right. It's an office that has obviously been ransacked. Go through to the next room, where there's an open secret door. Go through it, up the ramp and down the hallway into the last room, which is a storeroom of sorts. Look under the bottom shelf for a lever.
As for the doors, spoiler:I know there are some doors that just do not open in this mission. I think the one on the street is one of them. I don't recall ever getting the basement door in Bafford's Warehouse open, either.
I'm pretty sure the gate with the broken switch that you mentioned doesn't open, though not positive.
The door to the mine doesn't open. When you've completed all the other objectives, go back there and the mission should end. You don't actually get into the mine.