EBEACH-
Congrats on removing the inner liner section of the transom. I can not wait to see the project within the next few days, I hope.
As for your scuppers, I would suggest routing a drain hose from two new cockpit drains on each side of your aft deck, add one way valves to the drain hose and exit out the transom. cover the transom exits with Raboud cone style ball flaps
Cockpit drain-------check valve------exit/Raboud