You dont need to do the controller thing for mine. I tried it for a while but didnt see any difference.
For injuries, all you need to do a separate save of the franchise at the end of each week. Play out all the games cpu vs cpu. You will get no injuries of course. Then go back to the save file you have at the end of the previous week and sim the week you just played out. Record all the injuries. Then go back to the other save file that had just finished the week playing out the cpu v cpu games.
You will have to sub out the players from every position that they could possibly fill prior to the next game. eg. A LG must be taken out of all the lineman positions, TE, and the LS positions. Once you take him out of the top 3 spots at each position he will not be put in the next game you play out with this team (at least I have yet to see this happen).
Just make sure that you sign adequate FAs to keep your roster healthy as the game will not queue you to do so here as the injuries that you have are not recognized by your game.
This isnt entirely accurate as the player is assumed to have gotten hurt at the end of the game....not realistic but it is the best that I can do.