1. Injury time is simply the time during the game that action was stopped due to injuries and so forth. Just like in a real game, FIFA will tell you how many minutes are left in injury time (but will not show the injury time ticker).
2. Yes, if you have to substitute a player, he can not come back in. And you only get 3 substitutes per game.
3. Best team, you might have to break it down by country:
Spain - Real Madrid, Barcelona, Athletico Madrid
Italy - Inter Milano, AC Milan, Juventus, Roma
Germany - Bayern Munich, Schalke
France - Lyon, Marsailles, PSG, Bordeaux
Netherlands - Ajax, PSV
Scotland - Glasgow Rangers, Glasgow Celtic (The best rivalry in sports, period)
England - EPL is a really deep league, you could realistically win the league with about 7-8 teams. Man City, ManU, Liverpool, Chelsea, Arsenal, Tottenham Hotspur, Everton.
4. Yes there is a Career Mode where you can start a a player, a Player/coach or as a Coach.