Great your staining and waterproofing all the wood. However cedar is not a hard wood, in that it will crush under weight (read your boat motor will fall off in rough seas), it won't hold screws under load, etc. It will last forever in the elements without treatment and makes great fences, shingles and siding. In other words non-structural applications.
For your transom, go with Teak or White Oak. Check your local lumber yard for pricing, neither are cheap, however White Oak should be a native species and might be less expensive. White Oak will last forever in the elemets without treatment, plus it is a very hard wood. It will support your motor and strengthen your transom without any troubles. Dont get RED Oak, it doesnt have the same weather resistance as White Oak. White Oak has been used for ship building for centuries.