When you release a player, do you get a hit on your salary cap in terms of paying for part of their contract?

If you have that value set in the options, yes. It's configurable.

How do you alter it? Is it the 'drop penalty' option where you select a percentage or is it somewhere else?

Yes, that's it.

How do you move players from 'Injured Reserve' back to the Roster when they are fit again?

Once players go on IR they are not eligible to return until the next season. If you expect them to return you can put them on the practice squad.