Brad covered most of the points about using wood.
However, you might go a bit further.
Take your wood, and cut the transom board to size, using your old one as a pattern.
Then, drill all of the holes that need to be drilled in the wood, i.e. motor mounting holes, bracing brackets, mounting of the transom board itself.
Then, take the board out of the boat.
Now, take a good water proofing compound - immerse the board in the compound and let it sit for a week. This will allow the compound to completely waterproof the board, as well as the drilled holes etc.
Take out, and let dry for a week.
Now, go ahead and mount it in your boat. If you have an aluminum top cap - be sure to use a good marine calking compound spread liberally across the top of the board, before mounting the aluminum top.
If you have splash pan drain holes that are metal lined - be sure to use a good marine calk - to completly cover the wood, before installing the metal hole liners.
Bottom line - water will get to the wood in a boat.
If you don't want it to rot - you need to insure that there is a waterproofing or calking barrier between the water and the wood.
Take care
REW
p.s.
In past years, I have toured a couple of different aluminum boat companies, that had a very long guarentee on their boats and transoms.
The afore mentioned process was the exact system that they used in their new boat construction. i.e. cut out the wood, drill ALL holes, soak in waterproofing compound for a week, dry for a week, and then build the boat, using good calking in necessary areas.
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