May I make a suggestion prior to installing that transom since you are using wood. Cut a large 1/2 hole where the drain plug will be installed. Install the transom then go back and fill with Epoxy to where it is level with the surface of the transom core. Once that is cured, drill the epoxy and install your transom/bilge drain tube. This way there will be no water absorption later as the wood will wick it up like a candle wick. Sort of the same as over drilling engine mount holes and filling with epoxy and redrilling for permanent install. Much easier to do while out of the boat then trying to drill it when in the boat.
One question, you are saying to use epoxy? Is this for the water proof properties of epoxy. Due to the fact I will be using poly could I use thickened poly instead? How will the poly drill? Also I am planning on painting the bilge bottom portion on transom, and underside of deck with an epoxy based bilge paint.
When you push on it it flexes in between 1/64" to 1/32" ... could it be drilled and injected with resin??