Re: Motor mounts
If you've read many of the other restoration threads, you have probably seen advice to drill test holes into the wood core of structures such as the transom (start low) and your motor mounts. If you replaced stringers and bulkheads, the motor mounts are most likely also rotten, and if the rot started within the transom from poorly sealed external hardware mounts or undrained bilge water, then the transom will be needed as well.
There are scores of projects here that have taken on that task, and reading those that have "been-there, done-that" can give you ideas, tips, and examples of things to avoid.
For your own use mostly, but also for the voyeurs here, take pictures of EVERYTHING from several angles before and during removal of any hardware and structure. It serves as a great reference and reminder when putting it back. Place a measuring device like a tape measure in the pic to record dimensions that are difficult to document on paper. Document all dimensions -- thickness, distances from static landmarks X, Y and Z.
And finally, post your progress here so the resident band of self-taught professionals (and a few actual pros as well) can lend a hand, answer questions and mostly, cheer you on.