I'm not sure how much ridership the S48 gets along South Ave since the S40 is also there and is much quicker, ferry wise, if ridership is low in that area people can always transfer form the S40/S46 to the S48.
For the south shore, I attempted to make the routes straighter and more direct, which attracts ridership. The S56 could take Arthur Kill - Arden - Woodrow like it does today instead of going straight down Woodrow if needed. Thinking of what you said early, a new route could go from the south shore via. Arden to Jersey Gardens but i'm not sure if that would be overdoing it for the south shore (since most people drive down there).
The S77 runs from New Dorp to Bricktown so Tottenville riders still have access to Bricktown. You could extend the S73 to Tottenville if money permits though but I wouldn't terminate the S77 in Tottenville since other south shore riders along Hylan use the route to go to the Bricktown Mall as well.
The S52 is one of the most meandering routes in the City, so shortening it and making it more direct would attract more ridership. The Area around Arnold street are less than a 5 minute walk from the S44 and the redesigned S42 as well. Maybe some short turn trips to Arnold Street can do during peak hours.
The S67 would be made by converting existing peak S61/62 trips, so that's why it operates rush hours only. The reason why I disagree with moving the S57 to Jewett is because the S57 gets a lot of ridership along Decker and Willowbrook/Watchouge. Especially from school kids using the route to get to the Schools in the New Dorp area. In fact, the bus is usually SRO on the early morning trips to New Dorp by the time it gets to Willowbrook/Forest.
I'll comment on your proposal later.