What is the seating order for 4 player team games? Does it matter?
You probably mean playing order. Mostly it doesn't matter but the "default" initial order is A1 B1 A2 B2 (A and B are teams, 1 and 2 are players) shifting clockwise after each turn (i.e. B1 A2 B2 A1 in the second turn etc.). If a different initial order is required it should be stated so in scenario rules.
Can you play 4 player FFA?
Of course. But if you want to use the main game scenario you should reduce the number of victory points needed.
In Free For all, do you choose who you want to take casualties?
I'm not sure what you mean. You should know that you can only fight one enemy at a time. If after you have moved all of your units multiple battlefields ensue you (as the attacking player) choose the order in which battles take place.
Well, there is a possibility for more than two players'/teams' units to share one space after using Town Portal. This case isn't properly covered in the rules. It is not clear whether all battles (including those not containing any of the current player's units) need to be resolved before the end of the current player's move step or if they can be resolved during one of the other players' move step. But the rule that you fight only one enemy at a time remains and other enemies cannot intervene.
What about team games, does the recieving team pick?
Yes. Team players decide how casualties are divided among their units.