I will try to tackle your first two questions since they are related.

You do not have to look only at hands/Sngs you win, but also at hands/Sngs you lose.

If you look at most decent Sngs players in midstakes they run about 1015% ROI with about 10% rake.
Player playing the $50+5 making 15% ROI means hero makes about $5-5.0 - 7.75 a game, lets assume 6.50 on average. If you pay $9 instead of $5 it means you make $2.50 on average, which is about 40% of the earning you made before.

Same logic is true for the rake, you dont always win, you lose some pot, if you lost 2 pots in which you invested a total of $7, and you won a $20 pot, out of which you invest $9 for example, you won a total of $4 over those 3 hands, paying $2 to the casino is 50% of your profit