Hey Mark - good to see you're still working on the Mac 25 and posting - hope the changes you're making are going well!
Question 1 - there's only one bolt but 2 holes in each, and never thought anything of it, and after 34 years, I still inspect them annually and all seems to be well...
Q2 - When I bought the boat new, it had the gaskets installed on the pop top. I've continued with that location, mostly because with the top up, the gaskets would get torn off the deck too easily. When you're out there sailing, things happen, and the less things that can get torn off easily, the better.
Q3 - The cockpit locket lid has always been a question in my mind. While pretty organic, it does the job. Knock on wood, I haven't yet had an issue. The other mac 25 guy in my marina doesn't even bother to lock the hatch or the lid, so he's no help with this question!
I look forward to hearing anyone else's answers on these questions, too.