RE-RE-doing my Scuppers

[TunaMeltdown]

I replaced my scupper (Floor Drains) in my 23' before last season. When I bought the boat they were plastic. I ripped them out drilled and hogged out the 1" holes through the block of wood. I allowed the wood to dry and then patched the bottom and filled the tubes from the top with thickened epoxy. Then I re-drilled the 1" holes and installed the Moeller drain tubes. I thought this would fix all my problems...............

Well after running the boat for an entire season, I have come to the conclusion that I must again reconfigure the scuppers/drains. Water comes in constantly, at rest, underway, and on plane. It has got to the point where I have given up on them and stuck drain plugs in them and for the remainder of last season relied on 2 brand new 1100 GPH bilge pumps. After having my 25' SeaCraft sink on me at the dock I am more than a little bit worried. I'm thinking about doing away with the drain tubes and filling them in again. Then I would try to re-rout the scuppers out the stern, right at the waterline. Is this something I should try myself? I have limited skills, built a custom pilot house and already redid the drains once along with various other things. I am just afraid that if I drill holes through a 36 year old original transom that I might be opening a can of worms that I can't handle. What say you?