A trader or merchant placed in a city
They can't move onto a kontor or a trade route space occupied by another player's pieces, but otherwise, no. They can go anywhere on any trade route space, moving as many pieces as allowed by their player-board progression.
It is the required order.
Yes, it is possible. You may claim a Bonus marker without placing a kontor. It is also possible to claim a route just to get the points because you control both cities.
Yes, but not during the activity in which you acquire the marker. The extra kontor is really only valid during the 'establishing a trade route' activity. But if you got such a bonus marker during this activity you can not use it until you use the "establishing a trade route" activity the next time. If you take a bonus marker from the board you immediately take one from the stock and place it on the tin plate. That`s important because if the stock is empty the game ends after this "establishing a trade route" activity immediately. And placing the bonus marker on the tin plate helps you not to forget to place this (or perhaps one or two more) bonus marker on the game board at the end of your turn. Bonus markers which are already placed on the board are never moved to another trade route.
You keep the bonus markers you collected from trade routes beside your personal panel. They are face up as long as you did not use the function of the bonus marker and after use they are turned face down. At the end of the game you get prestige points for face up and face down bonus markers beside your personal panel.
The displaced piece is relocated to any empty space on an adjacent route, then you may take a piece from the general supply and add it to any empty space on an adjacent route. Both pieces are allowed to be placed on the same route if space permits.
You may not replace if you have not the penalty for this action in your personal supply.
At the end of the entire current action. So you still can get the bonus marker, can build in the city or increase your privilege (for maybe getting the prestige points for the complete development of the prestiges) and so on...
First, not the cities but the kontors you build in the cities are scored. Second, you score all the kontors (if they are connected) of your biggest network. You may select one network of connected kontors. If you have two networks (not connected to each other) you may only score one of them. By the way you count your kontors! Thus two kontors in one city count as two.