If Player A has an 8 week recovery (listed as doubtful) and there are 3 weeks left in the season (poss playoff bid). Why doesn't the system allow an IR option? I'm not going to play him and it gives me the opportunity to get someone else in.

He could still recover for the playoffs. I believe the 8 weeks is just an estimate and some players recover faster and some longer.

I also believe the IR option only appears when a player is listed as out

Also, in my experience a player can be "Doubtful - 3 Weeks" and "Probable - 2 Weeks" the next week.