How fine did you sand the deck before pre-coating? Epoxy doesn't penetrate as deep as most people think.

If you decide to go the full route, the sander will tell you when you're into bare wood. You'll see the color and feel the difference. Once you're through the epoxy and wood, I would switch to hand sanding with the grain (strips). 120 grit. On accasional sponge down with rubbing alcohol will reviel the color. Alcohol rather than water because it dries fast. The bare wood is always going to look darker than any areas where you have epoxy left. In many cases they will blend peerfectly.

Assuming you used 1/4 inch thick strips, you have a lot of material there. Be cautious around any areas where you had to sand like crazy to get fairness (like on the sides of the coaming ) since they may be a bit thinner.

Rather than going crazy with the entie deck, you could sand the front or back for starters and see how it goes. The front deck is usually what people notice the most.

I can relate to you obsession. If it's really bothering you to no end, you should do it and it will work out fine.

I know on repair and refinishing on my own boats that bare wood is not far below the surface. I have had plenty of areas where I wnent through glass and into bare wood like nothing. Usually on pointed ends or shear curves.
So I don't think the epoxy is that deep into the wood.

Any strips the reviel extra spaces that need filling (no Durham's wood filler) . Either use wood slivers or let the epoxy fill it during the presoak or glassing operation.

good luck. Try to remain positive. Everyone makes mistakes.