Deck repair dilemma

[HookUp]

Couple of years ago I replaced the fuel tank on my 208 so I wanted to lift the floor for two reasons. One, to inspect and see how things are holding up, and two, to redo the silicone/caulking job I did to reseal the removable panel. I could have did a much better job so Im hoping so of you can offer some tips.
I will definitely be using blue masking tape to get a clean line but was curious on how thick or deep to lay the bead down. Anyone who has done this before knows the gap is as deep as the thickness of the floor panel.
Do start with a small cut on the tube and get the bead down deep first, or start with a wide bead and just "bridge" the gap?
Second is the condition of the floor panel itself. The gelcoat is well worn where my cooler sat and slid around for years, along with the panel edges where the glass is also starting to get exposed. Along with some tiny voids starting to show and hairline fractures near the edges. This is a 30yr old boat so I'm not looking for perfection but I am looking for a solution that will protect and last for a few years. Maybe some kind of paint?

Here are some pics:

 

[blindmullet]

Kiwigrip - I was in their page 12 years ago and getting ready to use it again. A little harder to clean but much better grip and easy application/repair.

 

[SkunkBoat]

For the silicone I screw the hatch down first and then silicone the gap. I don't advise putting silicone down and putting the hatch down into it. That will make it very hard to remove next time.
I pull the hatch EVERY winter. Inspect and clean tank and leave the hatch loose to dry out (while boat is covered.)
After using a razor blade to get the bulk of it, I use acetone and a scrubby to clean the surfaces.

I have recored the hatch but did not touch the topside. The surface is not as worn as yours but the non-skid is worn. I am thinking of getting some knock-off "seadek" type foam decking sheet and sprucing up the fishing cockpit rather than any kind of non-skid paint.
It goes down with 3m double sided tape. Seems like something to try before paint. I'm not talking the full custom Seadek but just buying sheet and doing it myself for a couple $100

You could touch up with epoxy, paint the edges, before covering with foam decking?
I have used Durabak on the deck of another boat and it was nice for a couple years but I would not go that route with my Grady.