Does the instance of the ram and board replace the free shoot or is the ramming ship still allowed to fire point blank with the captain ability?
All four things can happen, in this order: Move>Shoot>Ram>Board. That’s the order of operations when it comes to moving and ramming when the ship in question has the Captain ability.
In this case, the ramming ship can fire with the Captain ability, though thematically you can think of that happening as the ship gets very close to the other ship. After the shooting is resolved, ramming occurs and then boarding (if initiated) after that.
Do free actions stack when triggers happen.
I believe so, though Woelf will be able to give more clarifications on if they do and if there are exceptions.