1- I'm not sure about the trade routes, some of them may have changed a bit during the versions but there shouldn't be a hole in the middle. IIRC, the Persian Royal Road went from Lydia to Susa at first, so that may be the cause. Though I had thought there was a building in game in Persepolis as well.
4- The symbol is well known to be incorrect. Other symbols for the ruling dynasty have been looked for, but nothing has come up. The thought of using an early religious symbol was put forward, but the symbol of the later dynasty would be just as correct as a national banner as that would be.