Is there a way to indicate that you would like a particular lineup in or 'my best FT shooters, when up by X with X minutes "?

I haven't found anything and think this would be a great enhancement; particularly when you have a very good FT shooter who is a back-up but someone that might be your 6th/7th man.

In real life many times a team with a poor FT shooter will pull out that player late in games when they are ahead and know the other team is trying to intentionally foul. Then put in higher % FT shooters who play their same position but are not starters. Does not seem to be anyway to set this up in any fashion with HD: thoughts?

nope, but there should be

Your best free throw shooters are automatically put into the game if the situation dictates it.