1.I am afraid that it is currently impossible to cross rivers in fast travel mode, even if you mod yourself to play as a flying creature. You can, however cross over bridges, which are commonly found in towns built near rivers. When crossing a river in the local map, I generally follow this procedure:
i.Enter river and cross quickly.
ii.Move swiftly away from the river, in a straight line, pressing 'T.'
iii.Eventually you will stop receiving the message about not being able to fast travel because of there being a river nearby and you will enter the fast travel screen.
iv.Fast travel as normal. When you exit the fast travel screen, your companions will somehow be next to you.
Warning:Your companions might occasionally drown or be lost if you fast travel whilst they are too far away.
2.In the current version, human sites are the only civilisation sites in game. Thus, all characters (except outsiders, iirc) start out in human towns. This will change in the next version, when all civilisations will have their own unique sites. Also, to get a general idea of where you are going, press 'm' twice whilst fast travelling to bring up the world map. Note that the world map is not initially complete; you will have to travel towards the unknown areas to fill them in.
3.A few suggestions:
i.Don't travel at night-you are much more likely to be ambushed if you do. Instead, sleep until dawn in a village/lair. This will also, of course, reduce drowsiness.
ii.At first, try not to travel through the wilderness excessively. Try sticking around towns instead, so as to be able to sleep safely.
iii.Visit a fortress or keep and recruiting as many soldiers as you can, and as soon as possible. You can also find soldiers in towns occasionally. These companions will help you greatly if you are attacked. (ie. meatshields).
iv.Try to take easy quests first, such as killing a dingo in a nearby cave. Leave quests such as killing bandit leaders, night creatures and megabeasts for later. Also, if you are unskilled, it might not be a good idea to travel halfway across the world to reach a lair/town/etc.