I've been away for a while, but THANK YOU
@SailingCal21 for documenting this process, and thank you for documenting it here (where it can be searched and referenced in the future) and not on FaceBook. You will KNOW that the job was done right, or you'll know who to yell at for doing a shoddy job. You are also making this less daunting for any of us that follow in your wake.
Welcome back. Thanks for the words of encouragement. It has been a daunting task (on month 13 of a estimated 9 month project

), but I can see the light at the end of the tunnel. I'm trying not to think about the other deferred periodic maintenance projects (bottom painting, stuffing box repacking, fluid changing, etc) till the current task is completed.
Questions;
1. Did you consider replacing the embedded aluminum plates with G10? If I were to undertake this task, that would be my first choice.
I left the aluminum plates in place, but will improve the backing by installing 1/4" G10 along with thickened epoxy from the underside at each stanchion base. For the majority of the deck penetration areas I've used Coosa in lieu of balsa to eliminate the possibility of rot due to water intrusion. Originally, the cap shroud and jib car track had marine plywood which I've replaced with the same. After comparing the compressive specs for alternatives, I found that marine plywood specs to be better than or exceed alternatives, they've been encapsulated with epoxy to mitigate rot due to water intrusion. I'd be concerned about using thickened epoxy products as a sealant as it wouldn't have the "self healing" properties that butyl tape exhibits.
2. Around where the deck fittings mount, I would have placed a ring/bead of West System's Six-10 as a barrier in case of future water intrusion.
I'm using copious amounts of butyl tape around the fittings. I've found it to be the best to prevent water intrusion and to maintain flexibility over time. I've also masked off the areas where hardware is installed so that there's no non-skid under any fitting. My thinking is that the rough surface under each fitting is a source for eventual water intrusion, unlike a mostly flat mating surface
3. Also, way back at the beginning of the thread you spent time and energy cleaning up the old fasteners. Why not simply replace them?
Yes, that was pretty much a waste of time... educational, but a waste. Also, considering that I've added 1/4" backing plates, most fasteners now need to be somewhat longer. McMaster-Carr has been a godsend for sourcing SS fasteners and accessories.