First, I think your galley flat is upside down. Double check the manual but you want the side with the cut grove facing down, into the galley while the side with the stiffeners facing up.
As for the gap, I think mine was a little tighter but nothing perfect. My non-expert advice is to put masking tape on the side walls below the top edge of flat (on the galley side) to catch any thickened epoxy that squeezes through. Then put down a small bead of very thick epoxy to just fill the gap and level it with a scraper. Don’t force a bunch in there, just enough to bridge the gap on the top side to give you a solid surface. Let that mostly set (a couple of hours) and then put down the full bead with a fillet. Once you flip the shell and cut the galley hatch open you can fill the rest of the gap with thickened epoxy without a risk of it squeezing through. You’ll find some other posts in the forum where people kept trying to fill that gap on the first fillet but what happens is the epoxy squeezes out the other side and sticks to the walls in the galley never to be removed.
As for the stitch holes on the flat, they may be for the quarter panels but I can’t remember off the top of my head. Flip forward a few pages in the manual and read through how the quarter panels and transom are attached so you get an idea of how those will relate to the galley flat. The gap between the flat and the hatch stiffener doesn’t matter too much because they won’t be attached to each other once the hatch is removed (that’s why you covered it in tape) but you want to make sure the quarter panel can touch the edge of the flat and the edge of the shell when it is attached. You can hold that in place now to get an idea of how it is going to go together.
-mike