Here's the thread, back in July , where we discussed this problem... My small contribution is near the very end.... Hope this helps
https://www.microskiff.com/threads/sealing-cap-to-hull.54028/
"Backer rod" comes in 25' lengths and in various diameters, 1/4, 3/8, etc and is soft closed cell foam that compresses quite a bit in tight spaces. For a caulking tool I used an old 3" brick chisel and a piece of 1/8" thick board with a rubber hammer to tamp it into place. Add the backer rod while the first run of 5200 is still soft and it will actually aid in pushing the 5200 into place where you want it.
For those that consider a complete cap off job... Here's what you're facing... the deck cap is secured to the hull with machine screws spaced about 10" inches apart and through bolted to small lock nuts (at least on my old Maverick...). Before you can do anything with the cap you have to remove the entire rubrail (screwed into the cap every 8" or so... One of the shortcomings of most Maverick skiffs is that you can't remove the fuel tank without removing the deck cap (another or those "ask me how I know" deals). It was so onerous that I swore I'd never do that twice..... The caulking routine I've described above will seal the joint properly -it's already strong enough with the machine screws so strength isn't an issue - just the water intrusion when you're running in a chop...