Don't use rivets to install the access port. Use #10-24 stainless steel pan head machine screws with nuts and washers. If you use rivets, you run the risk of cracking the fiberglass hull or the plastic access port. Rivets also introduce a leakage path unless you use closed end rivets. Yes, you want to use RTV/silicone caulk when installing the new access ports and be sure to scrape off the old caulk first.
For the crossbar end cap covers, yes, you can probably find them around (I think I have a couple pairs laying around somewhere). The reason people don't use them is because, as you found out, the nylon screw has a tendency to become frozen in the end casting and breaking off. Yes, you could drill out and replace the screw, but most people don't bother. The later boats did not even come with this cover. It is purely cosmetic.
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