As far as drilling through that new transom I know the feeling. I didn't even want to drill the holes to mount the jackplate after all that work. Just treat it like an exterior portion of the boat.
I overdrilled the holes. Loaded up some 6" paint rollers and kept swabbing the holes until there was barely any exposed grain. Then thicken some resin and put a nice thick layer in there with your gloved finger, wait for cure and use your drill with a little smaller hole-saw bit with some adhesive backed sandpaper on it to sand it down to where your thru hulls with checks just fit. Very simple and goes quick.
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81 V20 1996 200 Ocean Pro
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