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I have done this many times, the best way to clean the holes is to grind with a dremel tool, till clean, don't worry if you get to raw glass!
Then like said above use a dowel of same size, about 1/2" shorter then the thickness of the transom, dip in resin to seal the dowel and glue in the hole, tap with hammer till it is recessed in 1/4 of inch.
Let dry top off hole and surrounding area with Marine Tex and you go to go!
Spread Marine Tex good so there is little sanding after, this stuff sands like Iron!!
Good Luck!
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