Thanks for announcing the plan for the future slow renovation of your newly acquired 15-footer. The Center Console model is generally a highly desired variant of the more common SPORT 15, so I would not go too far away from the present configuration in your custom woodworking replacement elements.
The 15-foot hull is a great boat; it might be the best small boat ever made.
The Yamaha 60-HP engine should be a good fit for the boat. After you run the boat for a while you may find that a re-powering may not be compulsory.
If you need advice on repairs to the hull, start a new thread in the REPAIRS & MODIFICATIONS forum for each particular problem you need advice on, or search for prior articles. For example, for advice on hull repairs see the FREQUENTLY ASKED QUESTIONS answer on that topic at
Q5: how is damage to a Unibond hull repaired?https://continuouswave.com/whaler/reference/FAQ/#Q5Reading all the FAQ answers is also a good place to start if you are new to Boston Whaler boats.
Once you have made repairs and modifications, you can start a new thread REPAIRS & MODIFICATIONS to show your work as you make progress.
The boat looks quite usable as it sits now, so I recommend to enjoy it on the water. That way you will get a better notion of what may need some refinement to suite your particular needs.
My hint to you is the seating may need improvement. Just about every 15-footer owner does something to improve the seats.